So:
- NA #1-3 establish who the Illuminati are and how incursions work.
- Secret Wars #10-12 is the conclusion to the original mini.
- FF #611 exposes Doomverse and Future Val playing with the bridge.
- Ultimate Comics Ultimates #4 is mostly about asshole Ultimate Reed and his City (I guess that mirrors the Doomverse above)
- Ultimate Comics Spider-Man #1 introduced Miles Morales.
Am I missing something?
Only reason I can imagine him being reintroduced at this juncture after his long absence from the run.
To be fair, Peter was unavailable before the timeskip, so he has only been absent for a few issues.
He'll probably have a part to play but I wouldn't read too much into his absence up to that point.
Hell, the most surprising part is that he'd be with Cap rather than with Bobby.