It's 99% obvious that the Mental Omega will show up in the final missions.
The Foehn debrief in Tainted Empire suggests that the Mental Omega does global mind control.
Foehn unit descriptions talk about some catastrophic event in the past tense, so something really bad happened.
In terms of the narrative, an Act 3 ought to happen, and it seems to be Foehn vs Epsilon after Epsilon defeats Allies and Soviets.
There are so many obvious hints in Foehn trailers, teasers from ModDB, Twitter feed that an Act 3, Foehn vs. Epsilon, is going to happen.
It'd be weird if Act 3 was hyped up and then no Act 3 happens.
No, you're hyping yourself up for something that's never been confirmed. Yes it's evident Foehn is a resistance against a world ruled by Yuri set some time after the conclusion of act 2. However, it's never been confirmed there will be an act 3. It simply implies there is an ongoing conflict after, which doesn't necessitate a whole other campaign. Stories can be left open-ended and vague, and have been before. I would say hold off on the act 3 talk for now. Because time and time again I've seen speculation become expectation and then fans get pissed about devs not delivering on something the fans made up but was never confirmed.