Proposal is as follows:
There should be a fourth option available at the end - and the beauty of it is that it would naturally branch in a way that satisfies both of the outcomes people are asking for.
Right now, the Guardian presents us with three options - destroy, control, and merge. Each are depressingly self-destructive in their own ways, and as we all know, we have no choice but to pick one. DLC could add a fourth option: REFUSE.
Shepard stabs a defiant finger in the Guardian's chest and declares it is not their right to "protect" us from the consequences of our own actions. If peace was forged between the Quarians and the Geth, Shepard cites that as proof that the Guardian's premise of inevitable conflict between synthetics and organics is wrong. If not, Shepard can simply deny the Guardian's conclusion and declare that we're going to go down fighting. Shepard delivers an ultimatum: take your abominations and go. Whether we live as a civilization or die by our own hand is a choice to be left to every one of us. So, f*** you very much, but thanks for thinking of us.
The Guardian blows off Shepard's ultimatum, and the Reapers continue to fight. At this point, the outcome is out of your hands. Shepard watches, unable to intervene, as the fleets continue to engage, the forces of the galaxy attempting to defeat the Reapers once and for all in conventional combat. The Guardian taunts you, trying to goad you into choosing one of the three options it offered, while assuming the forms of different people you've lost along the way: Virmire casualty, Anderson, and your love interest, dead or alive, just to screw with you. You can change your mind, or continue to stand and watch. If you gathered enough war assets (as in, much higher than the required amount for the "perfect" ending we're given now), the Reapers are defeated at horrific cost, but the Relay network remains intact, and Shepard gets to reunite with his/her LI and squad provided the Normandy survived the fight (itself dependent on other criteria). This would be the hardest ending to achieve, requiring the greatest effort and providing the most reward. You would really have to work your ass off to do this, but as evidenced by this poll, most of the people here would be willing to try.
If you didn't have enough resources, the Reapers emerge victorious, and, having defeated the combined military might of the galaxy, they are free to harvest everyone else. The cycle continues. They win. Either way, you get to spit in the devil's face once more instead of bowing to the invariably self-destructive choice he offers you.
Me: I personally think this solution would be profound. Furthermore, it really gives five endings for the game. If you we're not fully prepared for the war, then Shepherd allows the Reapers to win without sacrificing his integrity (which would be a major win in my book). Finally, if you were fully prepared then you receive the most rewarding ending possible with what I think could potentially be one of the most creative boss fights in gaming history...a battle of wills alone.