We really were gypped with Deanmon, weren't we? It was so fun to see Dean's character going in a crazy new direction after being static for so long. I wish they could have given us a scene of Cas confronting him before Sam had trapped him in the bunker. I would have liked to know what a Dean that's pure Id, zero empathy, and all the same memories would have had to say to him. I'm sure it would have been nothing nice.
As for ditching him at the hospital when he was crazy, it did seem a little cruel, but I'm not sure what other options they had. It's not like they could take him on cases, and Bobby's house might have been burned down at that point. Even if it wasn't he didn't really have the means to babysit an insane but powerful celestial being the way Meg did. A mental ward really was the most appropriate place for him. I found Megstiel as a ship pretty trite, considering how underwhelming their relationship is compared to everything that's happened between Cas and Dean (but since she was a girl and he was a boy it gets to be acknowledged by canon), but she did warm up to me with her behavior towards him that season. Dean certainly wasn't winning any points with his "nobody cares that you're broken" line. Though, the finale of that season gave us some excellent battle husbands fodder.
Castiel providing unsolicited information about feline genitalia will forever be one of my favorite Cas moments. And knowing instantly who the righteous bone belonged to by sniffing it. S7 did him dirty by trying to kill him early on, but they made up for it pretty well by the end.