Don't know for sure, but I think Conner appeared with Cassie last when he Died in the Fifth issue of the Infinite Crisis.
Conner wasn't in Smallville that long, but the few times we did see him there, he struggled with having a secret identity as a nerd. He didn't like having to pretend from what I recall.
Not sure why he can't. In the Previews of Adventure Comics he says he DOES have all the powers to Bart at the Titans' Tower. But it's certainly possible some of his Kryptonian powers are only still developing.
Conner has half of his DNA from Superman and the other half from a human template. That Human template is now known to be Lex Luthor. He also has a few extra powers that Cadmus doctors gave him as they were trying to mimic Superman's aura.
Hope this helps.
Personally, I liked the comic. I've added it to my regular monthly list. I don't like Cassie and I hope Conner stays girlfriend free for a while. Now Superman on Earth has me curious. So this story takes place after the whole New Krypton storyline? I hope new Krypton still exist. I'm glad Conner is staying with Ma Kent, she seems very lonely.