I was just thinking about this the other day while playing Alien Bash 2.
If I were to see a clone, I'd hope it would first and foremost play very smooth. Second it would have to look good. Third I'd hope for a more enhancements to multi-player mode, perhaps something that would required co-operative thinking in order to pass certain obstacles ...
Lastly, I'd up the RPG elements a bit, make it more story driven, give the players the ability to increase their experience level, more spells, etc. Sort of like an Action Final Fantasy or something to that effect.