My true problem with it is that when Mass Relays blow up (like they do in every option) they can destroy whole systems. So, everyone's dead anyway. Or, if you ignore that the systems are all destroyed, all those people are trapped in Sol, with a world that's so destroyed it'll have trouble supporting it's own people. Not to mention that Quarians and Turians can't even eat the food that can be grown on Earth.
It also makes no sense that Joker is trying to outrun that blast, because he should still be fighting with everyone else. Joker wouldn't just chicken out and run away, hell, the people on his team would want him to go find Shepard, no matter the cost. That's the established loyalty of Shepard's people (if you played the game in their favor).
And what's wrong with a cheesy stupid happy ending anyway? At least as an option, a choice.
Not to say that I didn't love the game, it was fantastic. But the last ten minutes are just total crap to me.