I didn't ship Emmett and Bay. In fact I was definitely in the minority around this board, but I still posted for a while. Even when I felt my interest in the show slipping away.
I was glad that Bay didn't end up with Emmett in the end, but I truly empathize with those who rooted for them. I liked her with Travis and felt that ending with them was the way to go. I liked that Bay and Emmett had a convo at the end, and he rode off on his motorcycle a la James Dean, which is how Bay referred to him earlier in the series. It seemed like they were doing a salute to Dawson's Creek, where Joey and Dawson tell each other they're soulmates, even though she ends up happily with Pacey in the end. Not very original, but I shipped P/Jo too so I was happy with that ending.
The Toby/Lily story stalled on me a while ago, but I like that Toby learned that there are different levels of retardation with Downs Syndrome and Carlton's life might be different than the one he feared.
John getting a paternity test and staying wasn't a big bombshell. Just shows that he thought Kathryn had cheated on him, but still loved her to raise Bay as his.
I understand the betrayal that Bay/Emmett fans feel though. They were jerked around the entire series. To add insult to injury, the final song that played was the same one Emmett and Bay slept together to, so that deliberate "gotcha" must have been painful. I figured that Daphne would end up with Emmett if they weren't going the Bay/Emmett route, since Melody and Daphne were always so close anyway. I was always indifferent to Mingo/Daphne. I was looking for an Emmett/Daphne scene since they're supposed to be best friends. They spent way too much time on the whole "bombshell" and Regina/Luca breakup. I can't even remember the last time Melody and Regina had a scene together, and they're supposed to be best friends as well.
For a show that started off like gangbusters and that I looked forward to watching to one that I didn't care if I missed ... sad. But since there's another ship I have from a different fandom that is the writers' favorite play thing to beat around and screw up, I know all-too-well how it feels when you as a fan are tortured and put through the ringer of horrible storylines.
Best wishes to all on this board and I hope to see you around
.