Bug, Ice and Grass types need a serious buff. A lot of their weaknesses don't even make sense... why are Bugs weak to Rock? Why is Ice weak to Rock and Fighting? They have a lot of other odd weaknesses, too. On the subject, I'd like to see Dragon types be given more weaknesses, because it's just not fair.
As for actual Pokemon, I do confess Water types in Generation V were SCARCE. Like somebody else said, if you didn't pick Oshawott you were confined to Swanna or Seismitoad. (You don't get Surf early enough for my tastes.) But, this was a flaw present only in Generation V (as far as I remember) so I wouldn't worry about it too much.
Like many others have said, we need more Ice types with more variety and decent stats. I prefer having Ghost and Dragon types being a minority (it's what makes them special!), but I wouldn't mind them becoming more common, either. BUT, either way, we NEED Ghost types to be available early into the game, because I love Ghost types and having to wait forever to get one without trading in is cruel. Generations V, IV and II didn't have any problem with this, although Generations I and III (from what I remember) did. Actually, I'd want a Pokemon from every type to be available before the second Gym. And have EVERY non-legendary in the Pokedex be available before the 5th Gym - it's just common sense, people! There's no fun in trading a Pokemon in as an egg (in my humble opinion) and otherwise, certain Pokemon are just unobtainable early enough.
Although slightly irrelevant, I do want to say I wish Gamefreak would stop clinging to the past, and just even out the stats of Pokemon already. Having one fully evolved Pokemon with a base stat of 385, (Beautifly) and another fully evolved Pokemon with a base stat of 600 (Garchomp, I'm looking at you) is just not fair and not fun. Buff up the weaker Pokemon and weaken the unfairly strong ones.
I mention this here because if Gamefreak would bother to fix old Pokemon before chucking out new ones, I'd want less Pokemon of every type because we wouldn't need so many. For example, if they would finally fix the base stats of Pokemon, I would prefer if they could have only 150 new Pokemon or so. If they don't, I'd want 200 more Pokemon to make up for this.