Extreme G 2 on pc loses the analog steering from N64, which turns out is a big deal. Throwback Entertainment made a port-of-a-port and introduced a speed hack in the launcher menu where you can slow down the game a bit, which helps, but doesn't fix the issue.

In some other cases like Hexen, there were alterations on console that I find generally more appealing, like an ost remaster or lighting effects.

The Genesis game Zero Tolerance and Dreamcast version of Expendable are games I prefer on console simply because of the control schemes on pc.