It was more of a close run thing in Europe, but Nintendo annihilated Sega in the USA and Japan. What with the Final Fantasy series, Secret of Mana, Chrono Trigger the SNES was incredibly popular in Japan. Plus you have all the other classic games, and it's plain to see that the Mega Drive was never able to match the sheer volume of the quality SNES games being released.
Towards the end of it's life, the Mega Drive had a bit of life breathed into it with the impressive Virtua Racing converted from the arcade machine... Nintendo hitting back with the massively playable, but slightly less impressive (graphically speaking) Stunt Race FX. Nintendo also made a big investment into Rare which started developing games like Donkey Kong Country, with the SGI workstations kindly provided by Ninty. As developers began to exploit the power of the SNES's specialised DSP processors, the Mega Drive was all but spent. :/