I'd say yes, from a character motivation standpoint.
He considers all mutants -- homo superior -- his equals, and percieves mutant domination as a genetic birthright. He would gladly accept help in opposing any threat to this percieved authority of his species.
Having said that, I'd rather not continue with the idea of Apocalypse being a real character, because it fundamentally violates the mood of the series.
Ultimate X-Men works because it keeps the focus squarely on the question of how mutants repsond to their genetic condition, in the face of pressures from various instituions: government, religion, the market economy, the mass media, and so forth.
Apocalypse -- as a megalomaniacal cosmic being -- doesn't work in that context.
Now, Apocalypse as the next step above mutants in the evolutionary ladder, that *might* work. Because, yes, it would provide a common 'predator', in the food-chain sense, for both Xavier and Magneto, regardless of their ideology. But *that* would be difficult to fit with the set-up Vaughn has already initiatied.