All in all, I think the second series was better written and more adventurous than the first. The only reason why I still prefer the first is that Chang was way better as a teacher who was, within Greendale's context, 'mad with power'. This time, he was just a pathetic lame bloke trying to fit in, and while the actor's great and there are still some funny moments, changing his character that way and Flanderise him that much was a criminal offence IMO. But I digress...
I think writing was genius, and the way they linked the episode with several plots and subtle sub-plots of prior events is just brill - amazing sense of continuity and attention to detail considering, for instance, the competitiveness between Jeff and Troy (e.g. the spaceship and the trampoline), Cougar Town (and very much in-character for those two to be there, throwing the shippers yet another bone), minor characters and their second-lasting breath-taking one-liners, the foe yay between the deans, the list goes on and on... I also liked the way Annie going (however briefly) for the third option mirrors Jeff doing the same on the series one finale.
For two years I've enjoyed Danny's outstanding acting skills and his extraordinary character so it's almost 'wrong' to pick favourites, but I think this episode was his best to date, for both the actor and the character - and that's saying a lot since he's always ace.
Also, I'm a huge Jeff fan, but I like the way this programme was more of an ensemble cast this series, and less Jeff-centred. The idea of him being the first to be eliminated was ground-breaking, especially for a finale, but for some reason if there's one programme that can pull that off without jumping the shark, it's this one. Lovely ending too - nice cliffhanger/resolution without soapie love triangles. Again, if there's a programme able to do that with style, it's this one.