Throw_this_away wrote...
It was referenced in ME2 that the ship scraps "dissapeared".
This was mentioned and then attributed to a number of factors, part of it being the Keepers and part of it being the unauthorized salvage. If I recall, EDI was created using a bit of said salvage.
As a result, most of these people will go running back to the arms of the council in ME3.
Heck, I made nice with the council the moment I had free reign on the Galaxy Map.
They are in for an ethical surprise. TIM may not look so bad in the end.
The Mass Effect series has a running theme where the player is given the choice to work to further inter-species cooperation or to emphasize humanity's ascension in the galaxy--giving Cerberus the Collector Base will probably be an integral part of ending the series with secure human dominance in the galaxy--against the Reapers and beyond, you know. Given the number of combinations between the choices you can make in ME1, ME2, and probably in ME3, I expect a lot of possible outcomes from preserving the Collector Base, some of which may seem more or less morally correct than others.
In my case, my character was a strong co-existance supporter, so she was strongly inclined to make nice with the Citadel Council and to cut ties with Cerberus at the first opportunity. It's obvious that the diplomacy-versus-domination divide that defines the Paragon/Renegade system is intended to underline and be underlined by the choice between human domination in the galaxy and human coexistence
with the galaxy, and that the Citadel Council and Cerberus are meant to embody those two extremes.
...I won't be in the least bit surprised if in ME3, one playthrough spends all of its mission briefings with the Illusive Man, another with the Alliance, and another speaking directly to the Citadel Council.