Ultron (MCU) was trying to help humanity evolve while Infinity Ultron sought to eradicate all life.

I'd say Demona from Disney's Gargoyles. I mean, there was that one episode where she traveled back in time and her past self met her future self.

Dr. Doofenshmirtz 2nd dimension

Oh, yeah. Although I much prefer the original Dr. Doofenshmirtz, mostly because Alternate Doofenshmirtz as I like to call him tried to kill him along with Phineas and Ferb. That was not cool.

Megatron X who was so awful, that the Megatron, seeing what he did not only disgusted and horrified him, but was also heavily implied to be what caused the main Megatron to mellow out and come back to his universe and save it from Starscream and not kill Optimus Prime after that, and eventually, leading to his redemption by the end of the Season 3.

Earth-98311 Hobgoblin is worse than his prime Animated Series counterpart.

Parallel world Diego Brando is worse than the original Diego Brando counterpart.

Emperor Nefarious is worse than Dr. Nefarious.

The first timeline Shang Tsung, Shao Khan and Quan Chi are worse than their second timeline counterparts.

Apocalypse World Michael is worse than original Michael.

2003 Utrom Shredder is way more evil than his 1987 counterpart who wanted to destroy the entire multiverse which would've result him being killed.

The Quentin Beck variant from What If… the Emergence Destroyed the Earth? committed so much more atrocities than his Sacred Timeline counterpart.