It's hard to pick a favorite between Genesis and SNES, because they each had their strengths and weaknesses. One of Sega's biggest strengths, in my opinion, during the 16-bit era was their main mascot games. Sonic just crushed Mario in the 16-bit era (talking home consoles, not portables). On the Genesis alone, between 1991-1994, Sonic had 4 games - 1, 2, 3, and Sonic & Knuckles. Mario, meanwhile, had just one released during that time period on the SNES - Super Mario World. If you include the Sega CD, that's FIVE games against one. And these weren't mediocre games either. These games ranged from pretty good (1) to better than SMW (2 and CD).

While SMW was a masterpiece, I just find some of the 16-bit Sonics more fun, and the rings system was a significant innovation over Mario. In SMW, if you get hit, you either die or lose strength, and power-ups are harder to come by than rings in Sonic. You get hit in Sonic, you still have the same strength and usually can go back and pick up some of your rings. It has a lot more room for error.

I know that SMW 2: Yoshi's Island also came out for SNES but it was outside the "core" 16-bit generation. PlayStation and Saturn were already out and it was an attempt to compete with them just as much as the Genesis. Although Super Mario Bros. 3 came out after the Genesis and Turbo Grafx-16, and the Master System and 7800 were dying off by that point so SMB 3 was really a competitor to 16-bit systems.

We all know where the competition went in the next generation, but I feel in the 16-bit era Sonic was just better than Mario.