Warning! tl;dr off the forward bow!
The thing with description is that it has to serve a purpose. Description is a tool that writers use to highlight things of note or to influence the atmosphere of a piece. Typically, if something is described in-depth, it's the author doing the equivalent of saying, "Hey, look here! This is important! Pay attention!"
The problem is, that when many people talk about "describing pokémon," they're talking about giving a blow-by-blow on a pokémon's physical makeup. This would be appropriate in some situations, but in general it isn't, and here's why: the character in any pokémon 'fic would be expected to be familiar with his world's native fauna, and therefore he or she wouldn't give any passing pokémon more than a cursory glance. If there was something unusual about a pokémon's appearance, they might notice it; otherwise, they're not going to dwell on the physical characteristics of the beast unless they've decided they need to inspect it for some reason.
Description is very important. Description in the terms of what most people on these boards consider it to be--talking about what something looks like in detail--is often not, and indeed can be quite a hindrance to a reader's understanding and enjoyment. Let's have a couple of examples. This is the sort of thing that most people seem to mean when they talk about "describing pokémon":
The gecko-like creature stood about three feet tall, and its body was covered in a layer of fine, glimmering green scales. A long, tapering leaf sprouted from the back of its head, and further leaves adorned its wrists and rump. Its underbelly was a striking ruby hue, and its eyes were yellow.
This, as I hope even the people who advocate such "description of pokémon" would tell you, is an absolutely sucky passage. They'd say (or at least, I hope they would), that the pokémon shouldn't just be standing there while the narrator discusses its physical characteristics; that's boring, and it wrenches the reader out of the flow of the story in order so that the narrator can drone for a few sentences about grovyle before diving back into the action.
And it gets worse! Sometimes, overzealous writers will go so overboard in talking about a pokémon that you
won't even be able to tell what it is when they're done with it! Observe:
The creature was bipedal and stocky, with thick, powerful paws banded with heavy black rings. A layer of thin, fuchsia fur covered its vaguely pear-shaped form, and two beady black eyes stared out from its squashed face, which was framed by floppy ears like isosceles triangles with the tops cut off. Jutting lower teeth, the same strange purple, overtopped another heavy black ring about the creature's neck.
I'll admit to being far worse at obfuscation than many of the authors here, but I hope you'll see my point in that this "description" is puzzling rather than helpful when it comes to determining a pokémon's species.
So what is "good" description, then? Well, what if the author wants to talk about what a pokémon looks like but doesn't just sit there and list qualities of it--or at least, doesn't make the listing so blatant?
The gecko-like creature hissed, showing tiny teeth like a forest of little razors. Its yellow eyes flicked between the travelers, and then it leaped from the branch overhead, flaring the leaves on its wrists as it soared across to the tree opposite. Jerry caught a flash of brilliant red underbelly as the pokémon passed overhead, the leaf on its head streaming in the wind, before it hit the far tree trunk with a heavy thump and clung on with its fingers and toes. It scuttled up the side of the tree a couple of feet before vanishing into a cluster of foliage, its green scales blending perfectly with the leaves.
There are times when such a passage might be appropriate if one wanted to introduce a grovyle to one's 'fic. However, remember that every word in a piece of writing should ideally serve a purpose, and those that don't should get cut. Description is all about conveying information--telling the reader what is important, guiding them to see what you want them to see in a particular passage. Let's have a look at what our two examples thus far tell us before seeing one more, what I would call the "correct" way to describe a pokémon.
First, our list-y description. What point does it eventually get across? That the pokémon we're looking at is a grovyle. Also apparently one that's sitting still and doing nothing while the narrator considers its virtues, but that's already been covered.
The description above is a little more complex. The reader should, hopefully, still get that, "Oh, that's a grovyle!" The passage does a little more than that, though. It lets us know that the grovyle's hostile towards humans, or at least towards this "Jerry"--at the least, it doesn't seem too friendly, even if it doesn't outright attack him. It also establishes a sort of wild, feral atmosphere. Grovyle is canonically an extremely rare pokémon, so one would imagine that Jerry must be deep in the wilderness, perhaps even somewhere unexplored, if he's going to be encountering grovyle in their natural habitat.
Before I tie all this together, let's see how I think people should go about describing pokémon:
The grovyle tilted its head to the side and chirped, yellow eyes inquisitive. Its scales were scuffed and hidden here and there under patches of mud and dust, and there was an irregular bite taken out of the leaf on its head, but though its crooked grin showed a few missing teeth, grin it did, and if it had had a tail, Jerry had the feeling it would be wagging like mad.
Now, again, let's examine what this passage conveys. First of all, yes, it's a grovyle--though here it's actually just named, which immediately conjures up a complete grovyle image in the mind of the reader. Moreso than that, though, it's a grovyle that's apparently fallen on some rough times. It's got a bite taken out of the leaf on its head and it's a bit dirty, not to mention that it's got a few holes in its smile. Moreso than that, though, this passage gives you a fair amount of insight into the grovyle's personality, or at least what it's projecting to Jerry as its personality. It's definitely friendly, and its manner also seems a bit inquisitive, perhaps even slightly eccentric--its smile is described as "crooked," for example, and it seems to be acting a little odd for a grovyle; it even reminds Jerry of a dog, to some extent, which brings on further connotations of playfulness, loyalty, and so on.
That's a lot, coming from so short a passage. What's more, it reveals more than just what the pokémon
looks like, and instead focuses more on the way it behaves. By calling the pokémon a "grovyle," the text immediately gives the reader a basic idea of what to work with, then goes about describing ways in which this particular grovyle is
different than others, rather than rehashing what the readers--or at least the story's protagonist--already know and wouldn't ordinarily think about, instead considering the archetypal image of a grovyle that they have already acquired through exposure to canon.
This is why professional authors, or at least the good ones, can often get away without giving a blow-by-blow description of their character's physical appearance. In fact, the really good ones can do so so subtly that the reader never realizes that the image they have of that person in their head is constructed almost entirely from elements of that character's personality that their brain has associated with particular physical traits. This is because what a character looks like usually isn't important--rather, it's
who they are that is the concern of the reader. You don't sympathize with a character because they have the same color eyes as you do, but rather because you feel connected with that character through their emotions and personality traits.
Therefore, physical description is usually only used in order to "point out" elements of a character's personality. A person's hair color could be described, but usually only if it somehow relates to an underlying theme of the novel that plays off color to an extent or to draw on our understanding of the connotations different hair colors usually have for a character's personality. Consider, though, what you might be able to tell about a character given their hairstyle. What if their hair was messy and unkempt? What if it was done up in a style that was popular twenty years ago? What would you decide about their character then?
Thus, character description is usually less about getting at the "what" than it is about getting at the "who."
But what about my saying that the second grovyle passage was okay "in some cases?" That talks almost exclusively about the pokémon's physical appearance, so why is it okay?
Because the purpose of that passage is
NOT to describe the grovyle. Instead, the information it presents says more about the human character, Jerry, than it does about the beast itself (besides what was already noted). But how is that possible, given that the entire passage is about the grovyle, and the (presumably) human character is identified only briefly and by name?
First of all, it suggests that he might be unfamiliar with grovyle. Think about it. When you see a lizard, are you thinking to yourself, "Oh, it's a small, scaly quadruped with a long, slender tail. It has eyes on the sides of its head and clawed feet. It's blue with black spots." Probably not, unless you've never seen a lizard before in your life. Upon registering the creature, you're instead going to think, "Oh, it's a blue lizard with black spots."
The care with which the grovyle's physical appearance is detailed in the passage suggests that Jerry is trying to figure out what it is. Instead of immediately jumping to grovyle, his mind is listing down notable traits and starting to cross-reference them with his knowledge of other species--geckos, perhaps. And, because this is the pokémon world, his unfamiliarity suggests several things--perhaps that this is an alternate universe fiction, where many of the pokémon species with which we're familiar are unknown. Perhaps Jerry lives somewhere cut off from the majority of the world, where grovyle is a fairly well-recognized species. Maybe he just slept through most of his biology/pokémonology classes and doesn't pay much attention to stuff about pokémon. For one reason or another, his mind doesn't skip immediately to "grovyle" when he sees one, and the narrator therefore has to point out details that will make
us think "grovyle," even if Jerry doesn't.
There's another possible explanation, too. If you've ever had a cat suddenly dart out from the bushes next to you and run across your path, you'll probably have experienced a reaction similar to, "Small furry very fast thing dark-colored doesn't look like it's coming at me--oh, okay, it's just a cat." Fear is great at sharpening the senses, and when we're startled our brains usually run into overdrive, picking up all the details about something that we might otherwise just glance at and dismiss as unimportant. If Jerry were just surprised by the grovyle, it would probably take him a couple of seconds to realize what it actually was, as the passage makes it sound like it was moving relatively fast, and for a moment his brain would just be pulling in data, not synthesizing it. If that were the case, the next paragraph would probably start with some comment referring to that creature as a grovyle, rather than being a paragraph in which Jerry considers that "weird thing" he saw up in the trees. This would convey the fact that he's on edge, wary, and uncertain in this environment. The description of the grovyle, therefore, isn't so much important because it tells the reader that the pokémon is a grovyle, but because it helps to convey the skittish nature of the protagonist, as well as, perhaps, let the reader feel a little bit of his unease. It's primarily atmosphere, and perhaps a little characterization for Jerry, depending on the circumstances, that this descriptive passage serves to illuminate.
So, that paragraph could be saying a lot--but relatively little of it has to do with the grovyle itself! In fact, the pokémon itself is probably unimportant, and if it does end up returning for any reason, it will probably receive further description detailing its purpose in the story.
In the end, I would encourage you to describe pokémon. In fact, I would say that it's vital, even if you don't treat them as human-like characters; the fact that they're
not being treated like beings with human intelligence, after all, is just the sort of thing you need to get at through a description of the creature's behavior. But please, don't sit there and describe what color a pokémon is and what, in general, it looks like, unless this is somehow unusual or otherwise furthers the story in one way or another. It's perfectly kosher to just say, "The trainer had a magneton," if there's nothing remarkable about said pokémon.