I recalled my write-ups for this thread, so I'm going to continue where I left off, following the same pattern as the Marvel vs. Capcom series. They started off with a solo series, followed by a franchise-wide game, and then a crossover between two individual series, so that's where I'm at now with...
TEEN TITANS VS. X-MEN
The set-up to this will be similar to X-Men vs. Street Fighter, and the X-Men side will be the same as that game - Cyclops (1), Magneto (2), Storm (3), Gambit (4), Rogue (5), Wolverine (6), Juggernaut (7), and Sabretooth (8).
There were nine Street Fighter characters in X-Men vs. Street Fighter, but to my knowledge, all of them had their sprites re-used from Street Fighter Alpha 2, so they would have been much easier to include. Instead, I'll stick with eight Teen Titans characters.
-Nightwing (9) - he was already in Batman: Knightfall, and he's traditionally associated with the team.
-Starfire (10)
-Wonder Girl (11)
-Cyborg (12)
-Raven (13)
-Beast Boy (14) - Marv Wolfman's run on the team is, by my understanding, the most iconic/memorable, so it seems easiest to base the Titans roster around that. Plus, all of the members in this line-up have distinct appearances and unique powers.
-Terra (15) - I haven't reached her first appearance yet in my read-through of the New Teen Titans, but her powers seem like they'd work well in a fighting game
-Deathstroke (16) - as the main enemy of the Teen Titans, by my understanding, it kind of feels like he has to be here.
I could have included Wally West as Kid Flash, but I wanted to get more than one villain in here.
The final boss would be Trigon. I could have gone with Apocalypse, I suppose, since he was the final boss of X-Men vs. Street Fighter, but I have the option for Wolverine to stab the devil in the face so I'm taking it.
This would be followed off with a fairly cheaply-made franchise-wide crossover...
MARVEL SUPER HEROES VS. JUSTICE LEAGUE
For the most part, the Marvel side would be the same as in Marvel Super Heroes vs. Street Fighter - Captain America (1), Cyclops (2), Hulk (3), Omega Red (4), Shuma-Gorath (5), Spider-Man (6), and Wolverine (7). (man, this roster was really weird in hindsight) The one change that I'm making is that I'm replacing Blackheart with Doctor Doom (8) - Doom was already playable in Marvel Super Heroes (so they can still reuse assets from other games), and when mixing up characters from these two companies, I'm not about to leave out its biggest villain. (with Omega Red, I'm guessing that they really wanted to bring back someone who hadn't been seen since X-Men: Children of the Atom, and Capcom really likes Shuma-Gorath)
For DC, I'll stick with reusing characters from previous games for the most part - Batman (9), Superman (10), Wonder Woman (11), Green Lantern (John Stewart) (12), Starfire (13), Lex Luthor (14), and the Joker (15). Starfire isn't part of the Justice League, but she's eager to fight, and I wanted to use some characters who had only made one appearance so far. One character is a partial exception - The Flash (Wally West) (16).
Wally would be a partial clone of Barry from the Crisis On Infinite Earth game - his suit would be darker red with a different belt, like his redesign in the comics, and as he has a stronger connection to the Speed Force than Barry, he would have a few different specials, such as lightning-based projectile.
The final boss would be the Anti-Monitor, re-used from the Crisis on Infinite Earths game. (X-Men vs. Street Fighter and Marvel Super Heroes vs. Street Fighter both had Apocalypse as the final boss - it's lazy, but some of these games reused assets to make it so they could get a new game made/released quickly)
Neither of these games would have much in the way of plot, largely serving as a vehicle for crossovers to happen. (and, in the case of Marvel Super Heroes vs. Justice League, to mix the rosters of several fighting games in their respective series together - characters like Omega Red or the Joker wouldn't have been in a Capcom fighting game for several years at this point)