Had a thought about Romulans in the FED: In the IDW comic that was the lead up to the Nu-Trek, Spock and others tried to save Romulus. However foot dragging (possibly done to "let them die") by the FED council led to the attempt to stave off the cataclysm being too late. In your timeline, perhaps that foot dragging didn't take place, and the FED helped to save the Romulan people, even when the proud Senate didn't want their help. Or maybe both major powers were too proud to help each other, but a brave group of FED and Romulan citizens, as well as members of both Star Fleets, moved heaven and Earth (er, Romulus) to save Romulan civilization. (maybe they saved most the people, but didn't save the planet).
The fall out of this would be loyal Romulans seeing themselves let down by their "noble" leaders and saved by an enemy, while the FED citizens would question their leader's commitment to the ideals of the federation. This could be the first spark of a schism in Federation society.
Your comment about the "big talky diverse Federation to run into a race that doesn't give too craps they are there and are going to "remodel" the galaxy to their liking", that's why the Borg was initially such a great enemy: there wasn't going to be some big debate or proving how assimilating other species was wrong. The only way to fight them was to FIGHT them, and given their adaptability THAT was going to be a challenge.
In Trek cannon we have a few powerful races way back who monkeyed with developing life: the people who inserted a message into the primordial ooze of various worlds; the Preservers who saved various species and cultures from extinction; and whomever built the Guardian of Forever. You also have whoever built the Doomsday Machine. Ok, the Messengers were the 'first race' so they might be off the list, but look at what you have left: a race that was trying to save life; possibly a second species that wanted to explore, move through or alter time; and someone that built a REALLY BIG PLANET-KILLING GUN!
What if it was all ONE RACE? Why would they try to hide little pockets of humans and proto-Vulcans and other species all over? Why would they need to see through time, and possibly alter it? And why would they need to destroy whole planets? Where they hiding species from some enemy, trying to predict it's movements and counter them with time travel, and if all else fails, send in a heavy hitter to destroy that enemy? And if all this was one precursor race, or maybe a group of races, what was the enemy like? (cue Inception horns)
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"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth