I really wish Shui Hu Feng Yun Zhuan had a grappling mechanic, if that was thrown in it would probably be the greatest beat 'em up behind the Bare Knuckle or Golden Axe series.
Yang Warrior Family really needs the throw damage redone. Throwing enemies does virtually no damage at all, rendering the whole thing useless.
Top Fighter 2000 would be amazing if they removed the stupid "B+Forward makes character freeze" thing. Fix that and put in a throwing game and you'd have probably the best original fighter on the MD that isn't an arcade conversion. A throwing game inserted into KoF '99 would make it loads better also.
Death Caliber would be friggin' awesome if it actually used the Justifier.
Double Dragon for MD by Accolade did so much right, yet the music sucks and it just plays like crap. At least it's better than any of the other Double Dragons on MD.
X-Men VS Street Fighter and Street Fighter EX + Alpha actually control halfway decent (I can pull out specials without problems), but the framerate is so jittery and jarring it ruins the whole experience.
Lord of the Rings 3 could have been even more cooler if they redid the sprites on the remaining characters, rather than just deleting them entirely. That's one of the few unlicensed titles that I consider a "good" game even when compared to licensed developers.
If Hercules 2, Mulan, & Pocket Monster 1 & 2 just got a bit more polish they would have been great platformers on the MD. Even in their present state they're a lot better than a lot of mainstream rubbish.