I would so dig a Reaper-win scenario. Just for the sake of watching it and having the motivation to replay everything from scratch, making the decisions with more knowledge and then kicking some Reaper-ass.
Besides, it somewhat was promised and expected... this could go either way. Just imagine a tough mission, you get to the end of it to learn that you can't finish it because:
a) you needed Krogan backup and Wrex is either dead or betrayed by you

Rachni have to sacrifice some of them to protect Shepard in his final stint
c) if Collector's base was saved, it appears and changes the tide of the battle with a huge collector swarm etc.
Damn, you could've gone epic with ME3...