There are more things to consider, though:
The static nature of the shift registers of the SNES controllers allows the button reading cycles to be spread along the code. You can do that on a Genesis controller but you must take care for the internal 3ms timeout that resets the sequential logic of the button multiplexer.
The cross layout of the SNES action buttons provides the ability to emulate two controllers at the same time, and that is a winner for games like Robotron and Petscii Robots.
One advantage of the Genesis controller over the SNES controller is the capacity to work on existing games (with the adaptor plugged in of course) (edit: that will require adding a switch on the adapter)