My most blatant instances:
Pit Fighter (Genesis).
Now, the arcade version of Pit Fighter is dogshit. And the SNES port is flaming dogshit. I personally find the Genesis port somewhat playable. I actually liked it enough to buy it, and I played it and beat it fairly regularly. The hit detection is a bit better than the arcade or the SNES.
Clay Fighter (SNES)
Definitely not the best fighter, but I enjoyed the imaginative characters and the opening song. I liked it enough to buy the sequel, and prompted me to buy Clay Fighter 64 1/3 Sculptor's Cut from my local Blockbuster when they made it available.
WWF In Your House (PS1)
I loved the Wrestlemania arcade game and PS1 port, so I had to get this sequel of sorts. It's not as good as its predecessor, but I liked it well enough.
This last one is video game blasphemy:
I love Chrono Cross, even more than Chrono Trigger.
I don't know if that qualifies, though, since Cross isn't really hated.