Djinn makes a decent point about Cloud's limit helping in the final battle. In fact, if Cloud has a Blade Beam set to go on Rydia, my original scenario where Cloud one-turns Rydia probably works and Commander wins. Thing is... who would be giving Cloud this limit (assuming enemy AI is perfect and knows it's trying to have the dungeon win, not the specific fight)? S1 Luc might do some damage with an MT attack, I suppose. Fight 3... since both Cloud and Yuri have revival, and Yuri is surely blocking paralysis (among his many other status immunities thanks to 3 slots), team FFT's strategy is going to be something like "Arm Aim Cloud, shoot up Yuri and hopefully somehow kill him through the healing, returning to Arm Aim Cloud when/if that runs out, then keep Cloud locked down with Arm Aim and shoot him up too." If this strategy manages to kill Yuri, then Team Commander has already been horrendously unlucky since Arm Aim Cloud worked first time or something, and Bowser can Terrorize down their damage. But the only way that Cloud gets a limit is if Cloud got shot down to low health, but then recovered from Arm Aim and healed himself. Having Yuri simply live, or Cloud die, and things don't work. Actually an interesting issue, since if you assume Cloud does need a limit, does some kind of taunting strategy where Cmdr intentionally lets Yuri die to lure them into giving Cloud a limit work? It's fraught with peril, that's for sure.
Anyway that's the last chance, since Cloud is going to get Stop-locked in fight 4, and will only take damage if he's literally the only one left alive and the Gullwings are cleaning up. So yeah. I don't think Cloud will be able to limit, alas, but it'd definitely help.
So, thinking more about it, yeah, I don't think Commander can beat the final fight without a limit and without Toad seriously disabling Rydia. So a dungeon vote there.
Standing by my vote for Team Shale; Tidus and Millena are cheaty.
Also going to vote dungeon against Team Piggyman; Tidus's initiative Haste on Benjamin is awesome, but the problem is that both Magus's damage and speed are worse in Floor 4 thanks to Ayla existing (and Lucca getting the Taban Vest). Robo is meanwhile at like 62% average speed. Magus & Ben need to get the drop everytime and do their magical MT thing, but a lot of the dungeon fighters are really fast, probably faster than Magus. Anybody who outspeeds them, or survives their magical onslaught, hits Tidus. And then fight 4, the Suikoden 3 fight, is just a nightmare. Hallec & Augustine are a lot better than I thought; they have speedy big damage attacks, and Chris's Silent Lake goes off really fast too. Even if somehow Magus could outspeed Silent Lake, Chris would probably survive their onslaught anyway, know that SL is useless, and Phoenix Rune somebody instead.