I don't know... Personally, I have no regrets about shooting Kenny in the end. I mean, I wanted to still have hope for him, I wanted to have his back... But eventually it became impossible, and I pretty much knew I had to leave him. And when Jane in the end arrived without the baby and told me to pay attention what happened next I already knew what she was trying to do. I knew the baby was probably fine and that she was only trying to show me how far gone Kenny was and she felt it was better to do it now in a generally safe situation than have him go off at the wrong moment. And while I tried to prevent the inevitable, when the time came... There was no doubt in my mind... And I shot him. And when Jane showed that the baby indeed was alive, I forgave her without a moment's thought. It was a brutally direct charade sure, but it was necessary considering the circumstances.
I guess that's what differed between my Clem and Alex' Clem. While generally I tried to make my Clem do what was right and decent and honest... My Clem had lost her innocence. She was prepared to do questionable things if she believed it was necessary. In fact, my Clem would have acted the same as Jane at the end, given similar circumstances... But she's not as far gone as Jane, she's still an emotional and empathic girl at her core, which is why I still decided to let the family in at the end of my ending... She still willing to still believe in people, but she's also willing the make hard choices if necessary.
Overall, my feelings about the season seems to be very different than yours. Whereas the first season high alot of high notes, it was a bit scattered (I mean, it even had a stand alone episode in there, which, while good, felt really out of place). Season 2 however was more focused, both in terms of each episode tying directly into the next and also on focusing on Clem's personal arc more than a group arc. Season 1 was an ensemble piece, whereas season 2 was a character study. Sure, the emotional highs weren't as high but Clem's portrayal, or atleast my Clem's portrayal, as a girl forced to mature too quickly and therefore a bit internally conflicted was overall more interesting than the slightly more simple arc she had in season 1. That's not to say that this season was vastly better or anything. Season 1 did have those highs which probably wont be matched ever, however season 2 was more consistent and focused. Less puzzles too which didn't suck (season 1 puzzle usually felt more like padding than anything). Overall I feel they're about equal, although for different reasons.
Also, for the record, I had way more conversations and scenarios in the first season that didn't line up with my choices than I had in the second so I guess you not experiencing that until this season just meant you just ended up making the choices the devs expected in season 1.
(also, considering how open ended my ending was, I can't see any way next season WOULDN'T pick up where it left off... although with so many available chooses it's gonna be a bitch to figure out. also, if it doesn't continue Clem's story, I currently have no interest in continuing this series. Clementine is this series and a series without her is worth absolutely nothing to me)