I think the idea of a Combo Meter (they could call it a Smash Bar or Meter or whatever) that rises when you combo and lets you use your Final Smash would be perfect. Whenever you pull 3 moves of in succession without letting the target hit the ground it starts to rise, more and more with each successive move. If you get comboe dback, you lose Energy instead. And just so 2 Final Smashes couldn't activate at once, once a single Smash Guage was full, the others could get ALMOST full but never truly fill until the filled player used his attack. The only flaw here is that people would spam Jab combos, moves like Fox's D-air and F-air, and falco lasers.
Anotehr cool addition would be ammunition. This could cut down on spam greatly, withe each character having a certain number of lasers/arrows/bombs, etc. they could use before running out. This would reset after they got killed.
Finally, I think that Final Smashes should be more balanced if and when they return. I dont just mean Sonic/Fox, Falco, Wolf... I mean characters like Lucario, Pit, etc. deserve better.