I really like Bisharp, Durant, and Mandibuzz, but you can't find them until so late that it's just not worth leaving an open spot in your party for so long, not to mention the crazily late levels they evolve at. Seriously, fifty-four!? Why would they even do that?
See also: Larvesta. You can't get it until you're able to use Surf, and when you do, you have to hatch it out of an egg, meaning you get it at level 1. And it evolves at level 59. Seriously, WTF?
AND, on top of that, if you do take the trouble to train that little fire bug all the way to 59 and evolve it... After you defeat N, you go into the Relic Castle only to find... a level 70 Volcarona?!? Then you facepalm, knowing that the time you spent training that Larvesta was a waste, that you could have just caught this Volcarona instead.
Well, at least that Volcarona can potentially help against trainers like Alder and Cynthia... provided you haven't already battled them.
Anyway, what should also go into this category are Pokemon that are so f***ing hard to find. Like Chansey in every game before Diamond/Pearl. Or Heracross in G/S/C. And there was one neat little idea I had in White: create a triple battle team composed of the three elemental monkeys, except all female and named after the Powerpuff Girls. Only problem is, two things. First, the monkeys themselves are hard to find (save for the free one you get in the Dreamyard, but that's only one). You have to wait for shaking patches of grass for one, patches that might contain Audino instead. And on top of that, they have an 87.5% chance of being male. After searching for hours for just one female monkey, I just gave up. So much for that idea.