The first that comes to mind is Strider Returns, Sonic 3D Blast, X-men 2: Clone Wars, any Spider-man game after Spiderman vs. the Kingpin 1991.
Strider Returns:
The original Strider is one of the best games ever made IMO. Capcom made this as an arcade and it got ported to the Genesis faithfully. Now take strider and give him bad controls, slow response, no robots. Take away the cool flowing level designs enemies and bosses. Not put him into crap levels where you fight little robots and explosions that are made only to anger and annoy you. Now you have Strider Returns, a game that you could not pay me to beat.
Sonic 3D blast:
The original Sonics are great and evolved with each title. You get to Sonic 3 & Knuckles a masterpiece! Now what do we have? A 3D Sonic game? Now we are talking! Let's get started! Wait, the point of every level of the game is to recue some birds 5 of them put them into a ring, then save 5 more birds put them into a ring then fight a boss with crappy game play and isometric fake 3D that is harder to control and can give you a head ache.
To defend the game, the boss fights are actually good, the bonus levels are fun to me and at least different than the other sonics and graphics look kind of cool. Still, a crappy sequel.
X-Men: Clone Wars. My favorite part about the original X-men game is that you have a limited amount of powers and have to save them and use them wisely. They were very powerful. In this sequel, you have unlimted powers but they are dumbed down and weaker. As you play you will find out that the levels and game play actually have been taken a notch down and it plays like SMS versions of Xmen, just as Sonics, streets of rage, altered beast, and many other games on the SMS that are inferior to their genesis counterparts in looks and gameplay.
Spiderman vs. the Kingpin is a complex game in a good way with and has great control and game play bringing you classic comic enemies to you. Every other spiderman genesis game sucks. The beat'em up spidermans really suck as well. Fighting idiot enemies with cheap moves which would be ok if you had some moves you could use but you don't.
To add a little, Golden Axe 3 is not as good as Golden Axe 2. In GA3 the magic system devolved back to part 1's style which sucks. The dragons now suck. No dwarf. WTF! Enemies have cheap moves. Graphics and sound are not as good. The ability to pick an alternate path on levels does nothing for me.

