Lets see, something like this.... in order to stop the reapers, all civilizations would have to accept the idea off leaving the citadel and the mass relays, because the ultimate weapon against the reapers resides in overloading them or something related to that.
This way, all civilizations would have to go back 2000 years or more, because, without mass relays, travel along systems would take a lot of time, and all the potencial yet to explore from the citadel would be lost.
The keapers could also have a role, becoming some source of dangerous cyborgs and trying to stop you from destroying everything (+\\- 20 super keapers to fight would be interesting

)
at this point, the decision off destroying or not the collectors base could have a huge implication, because it would give humanity, throw cerberus an huge advance, letting them on the edge off galatic development comparing to the other factions.
In my opinion, there would be also other interesting point: the illusive man himself. Imagine that his from another civilization (an extremely old one), which the history is quite similar to the quarians, but in an much bigger scale. They created the reapers and were demolished by them. That he his the last survivor, which final mission is to take them out. And although he is not 100% sure, the main idea off how to destroy the reapers comes from him, and he only wants the base to guarantee human dominance....in that way, destroying the base in me2 would't have greater implications, only in your relationship with the guy.
That way, it would be a kind off great ending, everyone might survive, but probably never see each other again, some important decisions related to the romances, like staying with liara that might live until 1000 years or having a final moment and never to see her again (intergalatic intercourse goes wrong ).[smilie]http://social.bioware.com/images/forum/emoticons/tongue.png[/smilie]