I personally loved this episode and it was my favourite episode of the season along with 3! The ending you felt was the most meaningful is the one I went with even though I kind of regret the last choice I made but not going to go back and change it so sticking with my "With AJ in Wellington" ending.
I do agree with you on some points in that some of the characters just seemed to be there like Mike who didn't bring anything to the table and his turn just seemed to come out of nowhere in a meaningless way. I liked Bonnie in a way but her just hating me all of a sudden for not trying to save Luke enough was pointless despite the fact I did try and save him and almost died because of it.
I do think the characters in the first seasons were better although I wish Jane was in this season more since to me she was the best new character mainly because she got more development than most of the other characters who were there from the start and I didn't want her or Kenny to die but it had to go that way and my connection to Kenny despite his downward spiral got the better of my Clementine.
I am very interested to see how Season 3 goes now considering the various endings there is to Season 2. I enjoyed the season overall although it had its shortcomings but will still be getting Season 3 when it comes around, which I will guess will be end of 2015 possibly first half of 2016 or later.