Sega was never really a big deal in Japan, but to illustrate its faded influence here:
The other day I was in a class where kids were talking about their favorite animals. A couple of kids wanted to know how to say "harinezumi" in English (hedgehog). Since Sonic is called "Sonic the Hedgehog" in Japan as well (well, Sonikku za Hejjuhoggu), I figured I would point that out and everyone would realize that they already knew the English word. Except that, out of a room of thirty 11-year olds, only a single kid (and the homeroom teacher) had ever heard of Sonic. This is the same room of kids that when asked "What do you want for your birthday?" answered almost unanimously, boys and girls alike, with "game soft(ware)". So it isn't as if they don't play video games.
Meanwhile Mario is everywhere, including on the covers of some of the official workbooks distributed by schools to teach kanji.