I would concur that Mario had the most significant jump.
I would seem to think that the greatest improvement of the franchise in going 3D would be Metal Gear because the NES versions sucked (Moreso Snake's Revenge). This could be paralelled by other small franchises like Hydlide and to a lesser extent Shadowgate. I would say Sonic if you were to go from Sonic 3 or Sonic CD to Adventure, however there was a Sonic 3D title intermittenly that wasn't so smooth. Gex saw improvement in my opinion. Fighters = blah/blech. I liked Mario Kart better on SNES. Pilot wings = honerable mention.
In conclusion: 1. Mario, 2. Starfox, 3. Metal Gear, 4. Castlevania, and 5. Pilotwings
"Let justice be done though the heavens fall." - Jim Garrison
"Ask not your horse, if ye should ride into battle" - myself
