I'd like to throw a few pennies into this intellectual piggy bank, if you don't mind. Nothing pleases me more than seeing others asking questions, striving to improve, or just making an honest attempt to take criticism as it comes (although many writers abhor the latter).
Firstly, re-read, re-read, re-read! I can't tell you how many times I've thought I was done with a scene or chapter afters days upon days of typing and hand cramps associated with it and BAM--a typo or grammatical error catches my eye. It is for this reason that all aspiring fanfiction writers (and veterans alike) have beta readers.
Generally, a beta reader is a trusted friend or fanfiction enthusiast who works alongside the writer in the eve of the writing process. A beta reader can help with almost any aspect of fanfiction, I for one have learned how essential they are to the success of a story the hard way.
My beta readers are not only my friends, but they are also the ones who put a "perverbial leash on my ego," so to speak. Simply, while my elders tend to praise my work with nothing more than a second glance, my betas are eager to tell me everything little detail that bothered them. Often times they object to my constant habit of over-complicating the simple and offer plausible alternatives. But we have a mutual relationship of sorts; I am more than willing to offer my services as an editor to the fray.
If and when you do manage to secure a beta reader, remember the golden rule: You do not have to take everything they suggest into consideration. The converse is also true--if you insist on ignoring every single word of constructive nay-say, your beta readers will most likely opt out on the argument that you're too immature to want to improve. I know that I would much rather spend my time doing other, more productive things if I was in such a situation.
That aside, I notice that one class of Pokemon fanfiction has yet to be addressed in this thread: Crossovers.
In the fanfiction community as a whole, crossovers have a dubious reputation as being the anti-thesis of canon virtue and sterility. Contrary to popular belief, crossovers are necessary and can be very enjoyable if precautions are taken and the story itself is well-written. For example, Kingdom Hearts is in many ways an assortment of individual crossovers combined into a unique, unprecedented and surprisingly thrilling whole. Crossovers can add a new dimension to what was old about Pokemon (or any canon for that matter) and make it new once again.
The following guidelines can be applied to any series, not just Pokemon (I will give examples from a collaborative-crossover AU Naruto-Bleach fanfiction project one of my betas and I are working on. My examples will involve Naruto and Bleach characters for this reason):
1. Clichés are the enemy. This is one of the reasons crossovers aren't liked. Don't just make characters interact in order to appease your curiosity.
Seriously, come up with a storyline besides, "ZOMG NARTUO FEL IN SUM DIMENSHONAL WURMHOLE & HELPZ ICHIGO FIGHT TEH HOLLOWZ!!1!11" or vice-versa because if you favor this archetype, any attempt at writing will be seen as futile. Fundamentally, a shallow plotline is a bad plotline.
Take the collab I'm working on, for example. My friend and I separated five characters (Naruto, Kiba, Ichigo, Renji and Shuuhei; if you were wondering) from the rest of the joint-cast and focused on their issues as teenagers in Tokyo (ah, the advantages and prospects of the AU genre). Not to say that their friends don't have their own issues, or that their teachers are saints among sinners, but it's more inconvenient to approach a story in an all-encompassing manner; that would make things too complicated. Which brings me to my next point---
2. An overly-broad scope is unyieldy and pointless. Don't shift your focus from character to character constantly, it's a hassle to reorient oneself on a scene-by-scene basis. And please--select one setting for the fic and stick to it! (Unless the canon in question is something like Kingdom Hearts or Resevoir Chronicle Tsubasa.) That doesn't mean you should narrow the focus to twenty-plus individual musings and pointless soliloquys of two characters throughout the entire story, but don't go so far as to write a chapter single-handedly narrating fifty-someodd characters' thought processes and get nowhere in doing so.
3. If you are one for the "suggestive genre", don't be afraid to experiment. A word of caution: There is such a thing as too much of a good thing; crack!pairings and crack!ships have a tendency to generate an ungodly number of flames on some sites.
4. Avoid using more than two series at a time when possible. This is a rule of thumb; a jumble of multiple series involving hundreds of characters has a habit of confusing a majority of your audience unless you write with the skill and poise of an Oxford graduate. (Again, Kingdom Hearts and Resevoir Chronicle Tsubasa are exceptions.)
5. Don't keep affiliation uniform. If the characters are supposed to work together, don't make things harder then they have to be. They shouldn't agree on everything, but they also shouldn't be excessively distrusting of foreigners because "S/he's different than me". (Outside of reason, in regard to the occasional friction between two or more characters, of course.)
Also, do not presume that villains will instantly become friends and form "an alliance made in hell" in an effort to destroy the heroes once and for all. Each antagonist has their own personal interests in mind and would typically be unable to reach a compromise with someone as like-minded as themselves goal-wise. (This is not always the case. Usuallly, if some sort of alliance is made, one person or side is often "pulling the strings" and doing a bulk of the decision-making in comparison to the other.)
Remember, not all things are black and white; a good guy from one series can be manipulated by the villain of another under false pretense, etcetera.
I guess that's all I have to say at the moment. Feel free to add to this or comment as seen fit. =3
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