Guacamelee x Shovel Knight
There's Indivisible, at least.
Wet dream since 2004 or something.
PlayStation Move Heroes and PSASBR.
Nintendo vs Sega: Cardfighter's Clash (Mobile and NX)
Card Fighters' Clash is SNK's thing - but I'd love to see them do a crossover with Sega, and that would work fine as an initial one.
SNK x Sega is pretty much my ideal crossover - it would probably work best as a fighting game, but they have quite a few series and concept that could work together fot multiple games in different genres:
* for 1-on-1 fighting games, everything that qualified for Fighters Megamix and NeoGeo Battle Coliseum plus a few more that didn't make it to those series. For something with some story, I could imagine things like Geese Howard hiring Shiva from SoR2 as a bodyguard...
* for a more open-environment hack-and-slash, something like Golden Axe and Samurai Shodown could work together in a sword & sorcery environment
* or for a stealthier approach, Joe Musashi and any of the SNK modern-day ninjas
* Afterburner with Prehistoric Island's dinosaurs or Metal Slug's martians
* Phantasy Star and Crystalis working together as fantasy settings with a fair bit of technology
* might as well include the patron saints of their consoles, Segata Sanshiro and G-Mantle
* for something more meta, use Segagaga's Dogma as a direct adversary, and NGBC' Warez as a resource-draining hazard
Other crossover that could be nice:
* The first Sonic x Mega Man comic crossover had a nice structure that could work in a game
* the Capcom x SNK crossovers aren't done yet as Geese and Haggar don't get to fight
* why hasn't Capcom tried a Capcom-only crossover fighter yet based on the Marvel Versus gameplay, since clearly Capcom Fighing All-Stars and Capcom Fighting Jam didn't work?