I'm pretty happy with Hyrule Warriors, even if that is only a crossover of an IP and genre rather than two IPs coming together as one.
Nintendo Kart and Nintendo Party, I'm surprised these haven't been made by now considering the success of Smash Bros.
Nintendo vs. Capcom, that would be pretty interesting.
Metroid and Dead Space, I would love to go through a Dead Space-like adventure with the power and abilities of Samus.
Halo and Star Wars Battlefront, not so much bringing Halo and Star Wars together. Rather, having a game just like Battlefront, but with Halo.