Ironically that only happened with time. At the time, it was actually the more popular of the 2 consoles(except in Japan).
In fact, I've found a couple sources that suggest Sega took the U.S. market. The problem is that people focus on the final numbers, without understanding what happened at the time.
In '95, Sega stopped production of the Genesis right away, to focus on the Saturn, while the SNES had about 2-3 years of non-competitive sales, to more than catch up.
This is just guessing on my part here:
I think the issue was that Sega just had no experience with a successful console, while Nintendo knew, from the NES, to keep the older console on the market longer, as people aren't just ready to afford a new console right away. Sega kept making that mistake, they pulled the Saturn for the Dreamcast, just as development for the Saturn was hitting it's stride.
Now, years later, collecting seems to have put more importance on Nintendo's older consoles/handhelds than anything else. The same thing seems to happen with all sorts of classic collecting. One thing gets seen as more important than another, for whatever reason, and here we are with Nintendo and Sega dicussions.
Edit:
*unrolls old controller* Did I have some freak of nature controller or what? Thing has a 5 foot long cord. There was a video about the console wars and the guys at Retro Liberty were complaining about the length of Genesis pad cords, and then I see the picture at Wikpedia:
https://en.wikipedia.org/wiki/Sega_genesis