The only thing annoying about Water-types from the standpoint of a writer is that a lot of them are hard to use because, in realistic mechanics (similar to the anime), most of them are fish-like creatures that have to swim in order to battle. I guess that kind of cuts down on what you can use as a fic writer if most of your battles aren't on or around water.
And as much as I'd like to see a couple more non-legendary Dragon-types, the Dragon-type itself is an uber. For as many different leaders/elite 4 members that have employed Dragons over the generations, I wish there'd been a few more Ice-types to offset them. Just thank God no one's thought up the idea for a Dragon/Fire combination as the only thing to be able to defeat it reliably would be (as fire's weakness to water is offset by the dragon properties) another Dragon.
I'd like to see them mix up the types a little bit more, though. I've always wanted to see some more of the true elements (so to speak) combined with the Psychic and Dark types. Dark-types have done a pretty good job of it with Cacturne, Sneasel, Houndoom, Sharpedo...but I'd love to see a good Fire/Psychic or Electric/Psychic combo.
Same thing with Flying-types. So far, the only ones that are part-Fire are Charizard, Ho-oh, and Moltres - all generation 2 or earlier. Maybe I'm the only one that kind of thought that Torchic should have had a split evolutionary line. It's not like Fire/Flying would make such an uberish combination. In fact, it'd be weak to Electric, Water (a very common type), Rock. It'd be immune to ground and the Ice weakness would be offset. It'd pose a problem for Grass-types (there's too many of them and not enough of them learn the really good moves) and Bug-types, because most of the same things that are weak against flying (except for Fighting and Ground) are also weak against fire.
....and I still don't understand why the f*** Riolu and Lucario are half-Steel types. Can someone please explain that to me? It should have been Fighting/Psychic or Fighting/Dark. Do we even have a Fighting/Dark yet?
And one Pokemon that got on my nerves...freaking Sableye. I mean...Ghost/Dark? WTF? Why Dewford Mines? Most of even your good Pokemon only know Normal-type attacks at that point. Fighting can't hit it, Psychic can't hit it, Normal can't hit it. Aargh...
And Scyther...for being such a badass in the anime, its type combination utterly screws it over. Weak against Fire, Electric, Ice, Poison, Flying, and 4x Damage for Rock. Gawd. >_<
And, say it with me...for as much as Lance and his buddies seem to LOVE it and for all the crap we have to go through in evolving it. Just make Gyarados freaking Water/Dragon already. Water/Flying? WTF? You spend hours training a Pokemon that DOESN'T KNOW ANY INITIAL ATTACKS BESIDES FREAKING SPLASH for something that a Level 5 Pikachu can knock out in one hit with a Thundershock? And if they're not Dragons, why the hell do most Dragon Tamers have one?? >_<