I kinda hope each enemy Race stays unaligned with each other. I mean Bungie just got done with Halo, where each enemy race was part of the Covenant.
It would just put too much of a Covenant vibe into the game if they were forming alliances with each other. Each race having their own goals and intentions in mind makes them each feel more in depth and intimidating in their own unique way.
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I think if there were at least five alien factions at any time it would be ok.