So I've been thinking more about the Temporal Cold War and I might be warming up to the idea, no pun intended.
Going with my want to have one of Nero's crew escape, perhaps one of them is a Changeling/Undine/Suliban. One of the factions involved in the TCW could have intentionally orchestrated the events between Nemesis and JJ-Trek for the express purpose of creating a new timeline. Their reasoning behind it all was that a new timeline would give them new potential allies in the fight.
This would explain a lot of things. Why the Romulans were experimenting with subspace weapons and Borg technology, how Red Matter was created, etc. While I want to limit the time travel stuff as much as possible, this does sort of fill in the rest of the blanks and give me an ultimate "antagonist" to play against Spock-Prime. Knowing that the other side is "breaking the rules" will justify Spock taking more drastic measures in this timeline.