The Genesis controller matches better with the older Maddens' three-window passing. On the other hand, the SNES Madden '94 apparently has a lot more graphical details/presentation, from what I've seen on YouTube. I only own the Genesis version but will try the SNES since it's cheap.
The first Griffey has the best graphics of any 16-bit baseball game, and the player names could easily be changed to their real names with a little research, but the gameplay is flawed because even the best pitchers are lucky to strikeout one or two batters.