User blog comment:James12708/A possible Strategy Games/@comment-2250460-20121013222455/@comment-2250460-20121013224833

No, they wouldn't. The only ending where the geth and quarians become whole, so to speak, is Synthesis, and in that ending there would be no more war to speak of.

In Control the geth go their own rout, separate from the quarians (although they still share Rannoch).

So either do the logical thing and add geth as a different faction, or ignore the previously established lore and go with Quarians/Geth, but don't just keep it as quarians.