I'd like to think I'm equal opportunity. Even if a design seems weird in the next evolutionary step, there's probably a reason for it. And overall, I don't really care how they look as long as their designs aren't stupid overcomplicated.
That said, I can think of three:
Venusaur - I don't really care so much that it became an old, tired dinosaur of sorts so much that it just looks like it's really really flat. Like it was run over by a car a few times. That, and the appearance in age difference really does seem unbalanced. Bulbasaur and Ivysaur go from being youthful and energetic to burnt out and aged over the course of one (or two) evolutions. Compare this to every other starter (though Blastoise does look like a hardened older man, too).
Nidoking - The red/green promo art of Nidoking that Sugimori drew? Hardcore. The way he looks now? I could hug him. Nidorino, at least, always looks like he means business. And this is coming from a guy who likes huggable Pokemon (and huggable Nidorinos. :P). But there's a certain appeal to Nidorino that's just been consistent, even if he's been softened over the years as well.
Rhyperior (I think) - Ugh. This guy and quite a few other evolutions of 1st gen Pokemon in gen 4 are why the phrase "leave well enough alone" exists in the first place. Designs that are complex for the sake of being complex are not effective. It's even more perplexing considering the franchise itself follows a very "if it ain't broke, don't fix it" model. I'd rather they continue the rest of the series from here on out creating new Pokemon, like the 5th generation, than tampering with what they've got. Even if that means adding a mere 20 per generation due to creative bankruptcy.