Yeah but remember Michael never had to experience that. He'd been pretty much the most powerful being in creation(save for God and a few others) for his entire life and then suddenly he finds himself trapped in a cage.
Also consider this: it's not just Michael, but Adam as well. A normal human kid who wasn't meant to ever be imprisoned forever, etc. It's possible the emotions of the host body took a toll on poor Mikey.
Or consider this: who told us Michael was crazy? Lucifer. Is the guy trustworthy? Of course he'd try to paint Michael as unusable. Remember we never actually see Michael anywhere. Another reason for Lucifer to want Michael kept away: Michael already has a host body. Lucifer, even though he appears as Nick, didn't actually go into the pit with Nick's body, he had Sam's and then lost it. So they wouldn't really even need to worry about a host body since Michael was already in Adam.
If you want to talk about things that bother me then it is the assumption that Lucifer wants to destroy the world and cause the Apocalypse. Remember the chat Lucifer and Michael have at the end of the 5th season? Lucifer didn't want to fight, he didn't want to nuke the entire world. It was MICHAEL who was more insistent upon that. So actually yeah..I could believe Lucifer wouldn't try to start the Apocalypse. Of course it doesn't mean he wouldn't turn the world into his own personal playground, but it was pretty much a plot point that Lucifer didn't want to go along with the whole plan of the apocalypse. Since think about it..if Lucifer really truly wanted to destroy everything he could of just used Death to do that.
Also I am beginning to think Castiel is now the angelic version of the Winchesters. Where Sam and Dean tend to have all their friends die sooner or later..with Castiel it seems now guaranteed that any angel he meets is going to be horribly killed.