You and a lot of people missed one very important thing about Me3: the running theme through the entire story, in every mission -- even the Omega DLC, in fact -- is the redemption of heroes through self-sacrifice. Mordin (and possibly Bakara too) gets himself killed to cure the genophage (or doesn't, and agrees to screw over the Krogan for now). Legion sacrifices himself to give the Geth all intelligence (and maybe Tali kills herself if things end badly).
In the end, Shepard can either make the ultimate sacrifice to save everyone and make the world a better place (like Mordin, Kaiden/Ashley, Legion, Nyreen, etc) or he can screw over everyone and accomplish his mission and restore the status quo. That's really the choice you have: be a live soldier who accomplishes a mission or a dead martyr who changes the world.
Not missed, just recognition that it's one of a few competing themes. Sacrifice has always been a central theme throughout the series, it was only in ME3 that this became self-sacrifice. Of course the other great theme in the series is 'finding another way' - in fact this plays directly into the final choice - the Catalyst's solution won't work anymore by its own admission. It needs Shepard to shape the next solution, a better solution, to find another way of resolving its synthetics/organics problem.
This is where the choices idea falls down.
Shepard just accepts the Catalyst's options. Why can't Shepard argue that another way could be to retain the status quo, without the Reapers? Peace on Rannoch, if you've brokered it, puts a torpedo into the side of the Catalyst's argument that the chaos and destruction caused by organics and synthetics can't be resolved without their intervention.
Instead, you're press-ganged into going down the route of accepting the validity of the need for a 'solution'.
Personally, I'd rather have had the opportunity to argue the basis of the central premise of the 'problem', than being forced to buy into the logic of an intelligence that subscribes to the theory that the best way to preserve organic life from synthetics is to build some ultra-powerful synthetics that can then convert all organic life into synthetics.