Absolutely. This doesn't and won't steal MK's thunder. The audiences by large are different and have been since day one for all respective franchises.
Popularity and success have absolutely nothing to do with the competitive scene, and a lot of people overestimate value of pleasing the hardcore fans in relation to the bottom line (hint: all recent releases have been simplified to cater to a wider audience). Look where catering to the hardcore got VF... oh, back to where it started: JPN arcades. Hardcore fans are the most vocal though.
Few people realize that MVC2 wasn't a big success and sold nowhere near 1 million on consoles. Yet, it's one of the few games with long competitive spans. But why would Capcom, whose franchises have had a broader appeal, would want a collaboration with a franchise that's big in one out of the 3 markets? One that doesn't have a viable arcade market either nowadays.
It would've made sense in the 90's actually, so I should've elaborated on the ancient history part further. In fact, there were actual talks of SF Vs. MK according to Ed Boon. That was 13-14 years ago.
Going back to the issue of popularity, the 3D MK's were VERY successful in the US; the dwindling popularity I referred to was for PAL regions. In fact, they sold more than any of the Tekkens, SC etc. last gen in the region. Hardcore fans complained but it didn't matter because the games continued to sell, and were the only successful titles Midway put out. If anyone brings up how their local store had a lot of used copies, it's irrelevant. Used copies of Halo 3 were plentiful mere months after release yet the game was a massive success.
As far as the arcade popularity of 3D, Tekken 3 was absolutely huge, and unless you avoided arcades completely from 97-99, it's not disputable (and the PS version sold very well). Hell, the game had a fan service game with 99's TTT.. It's not a myth at all, and I am speaking strictly of the US market here. Prior to T3, 3D games were still a competition obviously though 2D games were preferred.
Lastly, the US wasn't the focal point for the market overall in the 90's. The Japanese market was actually huge and they had a market leading industry. Emphasis on the past tense since it's handheld country though arcades are still alive. Their global output is mostly me-too type titles hoping to achieve the success western franchise have. Look at Sony, a Japanese company whose first party elites are western games (GT being the exception).
All that aside, if the new MK takes the west by storm, Capcom will be knocking at WB's door. They haven't been shy about collaboration recently, especially with western developers. Technically, SF X Tekken isn't a collaboration but a mere use of the Tekken license in their own game.