[gjsman-1000]

Well, here's actually an easy way to rationalize part of it:

Sega doesn't represent anyone. They are in charge of their own games, and that's it. They feel free to allow, or disallow, people to do whatever they want with them. Also, Sega of Japan actually feels not that much love for Sonic and was surprised by his US success - they don't really care; but if you touched some of their other franchises on their home turf they'd have a little more bite.

Nintendo, on the other hand, has wildly successful IP in Japan and the US; and also represents all of the developers on their platform. All it takes is for one developer to complain that people are pirating their old 3DS game and Nintendo should do something about it, and Nintendo doesn't really need to disagree and cause a 3rd-party developer to be upset. It's an easy enough fix, takes little effort, is a reasonable enough request, and keeps the relationship happy.

Edit: Also, as I elaborate here, Sega has paid a price for lax copyright practices. https://news.ycombinator.com/item?id=36048593