Scyther over Scizor
That's the first one that comes to mind. Scyther was one of my favourites in Gen I, and I remember seeing Scizor being the first time I felt disappointed in the franchise. I didn't want it, and it didn't seem like an improvement. The cool, green colour scheme was gone. Scyther's head design had been compromised. The cool mantis/sword claws were replaced by pincers. Nothing seemed like a net gain.
I tried to like Scizor, I really did. Scyther was one of my favourites and a mainstay on my Gen I team. For years and years I tried to trick myself into liking Scizor. No dice. It's just never worked for me.
As for the rest? I'm gonna admit this comes from a very Gen I attitude, but what can I say? It's what I grew up with/my introduction to the franchise.
I'm not a fan of a lot of the Gen IV evolutions of earlier generation pokemon. Not to say they were all bad- they weren't. These in particular though? They all follow a theme. They evolved pokemon I previously had a soft spot for and they didn't improve at all on the design of the previous Gen I forms. So they ended up ruining a few lines for me.
Likitung over Lickilicky
I admit I have a soft spot for Likitung. It was this weird lizard creature that was also strangely adorable. The species was pretty much ignored by everyone in Gen 1, both in the games and in the anime. I think that made me like it more? I mean I rarely used it on any teams, but I always enjoyed having one around. Lickilicky is just doofy looking. Nothing about it is an improvement. That's really my complaint with all of these...
Rhydon over Rhyperior
Nidoking is one of my all-time favourites (and is my favourite if you catch me on the right day
) so Rhydon was always one I liked too. They're similar enough to Nidoking but with enough different going on to make them a cool pair of 'mons who looked like they could have a pretty cool rivalry. Rhyperior is just...over-designed. Rhydon hit a sweet spot between aggressive and simple that all of the best pokemon designs fall into. Not so much with Rhyperior. It's just a design that tries too hard.
Magmar over Magmortar
I get why people say Magmar is ugly, but I love it. For a lot of the same reasons I love Rhydon, really. If you catch me on a day when Nidoking isn't my favourite pokemon? The answer's going to be Charizard. I've always loved Charizard. When I first saw ads and Nintendo Power stories for this new "Pokemon" game? I immediately decided two things. I'd be getting the Red version and I'd be starting with Charmander.
Then I got the game and my first strategy guide. Low and behold, in the Pokedex section, was an entry for this strange Pokemon called Magmar who was a bit Charizard-esque. Warm colouring, fire type, lizard and dragon-esque features, and a flame tail! Like Rhydon and Nidkoing Magmar and Charizard seemed like two 'mons who went together well. Then the episode of the anime aired where Ash's Charizard fought Blaine's Magmar and I was hooked on the guy.
Then Mahmortar came out. Like Rhyperior it's an over-designed look. The rounder torso, the out of control head flames that looks like clown hair. The cannon arms. It's just all too much and too silly.
Electabuzz over Electivire
This one doesn't bother me as much as the others, because I don't find Electivire too terribly designed. On its own? It works. My problem here is more with intent. I get the feeling Magmar had the mess that is Magmortar thrust on it because they came up with a decent idea in Electivire and they felt they needed to give Magmar an evolved form to keep the parallel theme the two lines have going. Just speculation on my part, but that's what it comes off as from my perspective.
Again, sorry for coming off like a Genwunner with the list. These are just the most immediate examples that came to mind when I saw the thread. I'm sure if I looked into it deeper less "old man yells at cloud" types of examples will come to mind