And he has to build yet another team for ME3 (OK, actually most of the ME team returns) because he is Alliance now. At least the Normandy gets a sweet blue paint and gets rid of those awful Cerberus logos. Subtlety much?
Also, I don't think it's that particular moon, it's just a spiffy addition to his admittedly pretty great office (and it changes depending on the ending to boot). Still, it could be foreshadowing (again) about the importance of Klendragron, the dying star and Dark Energy, and the fact Cerberus kept an eye on it.
Doesn't matter that much anyway, it's pretty much confirmed we are fighting Cerberus in ME3. The only possible reason, hinted at in those awful comics, is that TIM is indoctrinated due to a bad case of being infused with plot device... err Reaper tech, which makes absolutely no goddamn sense whatsoever considering his actions in the second game.
Completely agree about the spoiler, that and the very final scene in the Normandy hangar almost made up for Reapernator. Almost.
And about ME3 being more involved, (apparently) you basically choose which race survives and which becomes Reaper fodder. Yep.