How it should have happened:
After Anderson dies, Shepard stumbles forward and activates the Crucible from the console (rather than being transported upwards). Then, all of the Reapers are 'deactivated' in some kind of stasis.
Then Shepard gets to decide what should be done with the Reapers - destruction, study and distribution of their technology, or maybe some kind of spin on the 'synthesis' option.
After the decision is made, there's some kind of epiloque for each major character and race, and then finally Shepard him/herself - the events of the epilogues are highly dependant on the choices made in all 3 games.
That's it. No fucking space-Casper, no relay destruction, no Normandy crash on Pandora.
/rant, going to bed.