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Apocalypse, Legion, Phoenix, and Magneto

Vs.

JL Superman, Zod, Faora, and Nam-Ek

*Jean is composite with feats from Apocalypse/Last Stand
*End of Season 2 finale Legion

Who wins

This largely depends on Superman, to be honest, and his speed. Because the mutant team has more than enough hax abilities to win (from teleportation, to matter manipulation, telepathy, telekinesis, shields etc.).

It would be interesting to compare Apocalypse's or David's reactions to Superman's. Apocalypse took around 15 seconds to respond to Quicksilver, from Quicksilver's perspective, which translates to a tiny fraction of a second in real time. And David caught a bunch of machine gun rounds in his hand while his back was turned. Granted, it's still not clear whether that was enhanced speed/reactions, or some reality warp that moved the bullets to his hand. Either way, he was able to react to it.

I'm backing the Mutants here, they have more than enough ways to win while theres only one reliable way for the Kryptonians to which depends entirely on how fast we believe Superman to be in relation to Apocalypse and Legion as mentioned above.