There are various Pokemon that come to mind. One of them is Emolga. Its sprites in the fifth generation had an open mouth that looked so ugly, it made the Pokemon less cute than it could've been. Also, its Speed should've been a bit lower, so that it wouldn't have been so annoying.
Design-wise, Chespin suffers from the same fate; it's a supposedly cute Pokemon, but its official artwork ruined it by giving it an ugly smile.
Pyroar had a lot of potential, but Game Freak completely wasted it by giving it a high Special Attack stat and a low Attack stat, while it should've been the other way around. Litleo is fine as it is, though.
Weezing's Special Attack should've been a bit higher than its Attack, because I don't really see it as a physical attacker.
If Rampardos was a bit faster, it could've been more menacing.
Glaceon could've been a great Pokemon if it had more strong Special moves, and if the Ice type had more resistances.
Luxray being Electric/Dark would make a bit more sense, because it looks so dark and it can learn good Dark moves.
Lilligant should've gotten the Fairy typing, and Whimsicott shouldn't. Lilligant looks far more like a fairy than Whimsicott does.
Emboar should've been Fire/Dark or Fire/Ground rather than Fire/Fighting.
I loved Speed Boost Blaziken at first, but now that it's broken, I wish it had gained a different HA, like Reckless or Flash Fire. Also, its Mega Evolution rubs me the wrong way, because of Speed Boost and because there's no Mega Sceptile/Swampert.
About Mega Evolutions, I think Scizor, Garchomp, the
[email protected], and to an extent Tyranitar shouldn't have received them. They were perfectly fine as they were. Also, Mega Charizard X should've been the only Mega Charizard.
Tyranitar is one of my favourite Pokemon of all time, but Sand Stream prevents me from using it. It has Unnerve now, but I still wish it had already gained something other than Sand Stream in the third generation.
Blastoise should get something like Slack Off, Recover, or even Milk Drink for reliable recovery, so that it can be on par with Venusaur and Charizard in terms of competitive viability.
Snorlax should get Slack Off. Just because it's Snorlax.
Also, I think Farfetch'd, Jynx, Dunsparce, Qwilfish, Sableye, Chimecho, and Basculin should've gotten a (Mega) evolution already.