I'm not sure if I missed something during the game, but I'm still wondering why the Alliance plays no part in ME2's story. Specifically, why couldn't I hand the Collector base over to the Alliance at the end of the game? Why did I have to either destroy it or give it to a terrorist organization? Does the Alliance hate Shepard, or do they refuse to acknowledge that he is alive? It doesn't make sense to me.

It's more the problem of the public perception after the attack on the citadel. The last thing they need while rebuilding is a 'rogue SPECTER' that runs around and preaches about those damn reapers, when in 'truth' it was just Saren that were the mastermind behind it all. They aknowledged that he was back but they didn't want to be linked to his crusade... any less when he was doing it in the terminus system that's outside of Citadel reach and so on. It's more of a convenience for the alliance.

" It's more the problem of the public perception after the attack on the citadel. The last thing they need while rebuilding is a 'rogue SPECTER' that runs around and preaches about those damn reapers, when in 'truth' it was just Saren that were the mastermind behind it all. They aknowledged that he was back but they didn't want to be linked to his crusade... any less when he was doing it in the terminus system that's outside of Citadel reach and so on. It's more of a convenience for the alliance. "

The bottom line: People in places of power, like to stay in those places. The Alliance doesn't hate Shepard, but with their newly gained loyalty and respect of the galactic community, they would rather go along with the "lies" that the Council is spreading in order to keep that loyalty and respect. The exception to this is Anderson, and maybe Admiral Hackett. Although we didn't hear much from the Admiral in ME2. 
 
The Council is just blind, plain and simple. They spread their lies to cover up what really happened in order to keep the peace, to keep people placated. They'd rather have everything calm and under control than having people know the truth and freak out. They couldn't play a really significant role in ME2 because the Terminus Systems are out of their jurisdiction. Government ships in the Terminus could start an all-out war.
 
All in all, ME3 is going to be VERY interesting.

That Turian Council Member is still a douche though.
 
 
I hope we get to punch him in ME3 
 
:D

" That Turian Council Member is still a douche though.   I hope we get to punch him in ME3   :D "