Prime example: Rhyhorn
Rhyhorn (Gen 1) - Rhydon (Gen 1) - Rhyperior (Gen 4)
Rhyhorn and Rhydon are great. I actually like using them for their decent defenses and having a pretty damn high Attack stat among gen 1 Pokemon. They also don't look half bad.
Then Rhyperior. Stronger than Rhydon, sure. But appearance-wise? WHAT THE HELL!? First off, the color is way off which is very jarring (Imagine if Gardevoir or Gallade, two very popular pokemon, were suddenly VERY off shades of nasty puke instead of a similar green to their prevolutions.) And that really scrawny part of the arm, it'd snap if it so much as tried to MOVE it's arm! Like what the hell?
Gen 1: Every pokemon was functional in it's own way. Elegant in their simplicity (just look at that picture in the starting post for this thread and how Charizard would be ruined if it was designed in Gen 4.) And whatnot. And come on, who can honestly hate pokemon like Sandshrew, Arcanine, or Starmie?
Gen 2: They got a little more adventurous, here. Xatu? Smeargle? Some were great, others less so, but the point was, it was largely more of the same. Sure, Azumarill, as cute as it is, just lacks the sleek functionality of, say, Raichu, but what can you do?
Gen 3: OH GOD WHAT AM I LOOKING AT!? Medicham!? What is this and why is it's ability so broken!? I despise Gen 3 because all the "Oh god I hate this design" Pokemon are leagues stronger than they should be due to their abilities. The few pokemon whose appearance I DO like (Torchic, Swellow, Altaria, etc) are, well, generally not even really worth using. Oh, and Ludicolo. I'll say it right now. Ludicolo offends me. My best friend died when he was 13 (will be 8 years ago this October) - and he was from Mexico - and he didn't like Ludicolo because it was stereotypically offensive. And I carry on his stance. Point being, I walked away from Gen 3 with... Gardevoir. That's... really about it. Oh, and they also introduced a lot of no-sense type matches simply to add more STAB options. Fire/Fighting? Really? Those don't exactly go hand in hand. Not like Rock/Ground, or Grass/Poison, etc. Fire/Fighting is seriously just "Here, handle some of your weaknesses better!" Like seriously....
Gen 4: Okay. So while they made some things worse (Rhyperior is just one example) at least their new designs GENERALLY weren't as atrociously bad as a lot of Gen 3. Sure, Chimchar is a blatant insult to Charmander (don't give me that "Sun Wukong tribute" crap, it just looks like a cheap Charmander ripoff coupled with the aforementioned Mixed type BS - but at least they balanced mixed types across all the starters. Torterra gets Earth STAB against Infernape, who gets fighting STAB against Empoleon, who double weaknesses Torterra with ice.)
Gen 5: I really can't comment. No money to play it.