I doubt Nintendo will sue them, Disney and Nintendo have a long standing relationship and have shared IP with each other many times in the past. The Let's Plays were a different thing, they figured they could go after us little guys with no one raising a stink. They want a cut of the ad revenue from the bigger channels. Not saying it's right that's just how it is, they didn't expect such a big backlash over it so they backed off on enforcing it strictly.
The Capcom/SNK thing was a different time, now we've pretty much established that no one can own an entire genre. The competition between the companies was good for both of them and SNK games play a lot different from Capcom games now. But they're still close enough for crossover games, and that's why we got Capcom vs SNK 2 aka the best 2D fighting game ever released.
Seriously, if you own a Dreamcast or have the cash to spare to download it for Xbox 360/PS3 you should check it out. It's so much better than Marvel vs Capcom 2 and I'm saying that as someone that poured most of the early 2000s into playing that game at the arcades.