Well, the first thing is Beckett letting go of Josh. I really want her to admit she knows he's not the one. Choosing Castle over Josh is great, too, but I like the idea that she knows that even if Castle wasn't in her life, Josh STILL wouldn't be her "one and done."
I do agree, Tink, that the ball is in Beckett's court. I'm going with she heard him, but it won't be dealt with right away. It might be cool if reveals to Castle that she would have gone with him that summer - that she dumped Demmings for him. Maybe it comes out while she's explaining to him WHY she's working so hard to keep him at the 12th - despite the new captain. Beckett is slower with the words, but she showed him the murder board she made while he was gone, and then revealing this info would show Castle that she's had intense feelings about him for awhile.
I don't see them jumping into anything right away either, Fairytales. Between the new captain and Montgomery's info, there's enough to make them hesitate. Kate especially: having Montgomery keep those secrets has to have messed with her trust issues.
At the same time, she almost died - again. That whole, life is short thing is also in the air, so that thought should also be effecting the relationship. I like the idea that they both know and acknowledge that the relationship depth is way more than friends, but also that they have some fears about the timing... definitely want kisses that's not forced or undercover. I like the idea of mutually conscious UST that gets occasional moments of relief from kisses they know shouldn't happen...
I do think Alexis is growing up. She has a serious boyfriend. While I don't see ANYTHING involving teen pregnancy, I think having Rick having to deal with Alexis a young woman dealing with how sexuality should fix in her life at this time could be fun. It also would give him and Kate something else to discuss besides the insanity of the cases, Kate's mom, and Montgomery. It could also give Kate and Alexis some nice scenes if Alexis ends up talking with Kate.
I like the Alexis thing because it could open the door to Rick's past. In one of Stana's interviews she pointed out that while the audience knows Rick wasn't the one who messed up his marriages, Kate doesn't. Rick and Kate talking about Alexis's questions about "when is it right" could lead to Kate realizing Rick's the one who got burned.
Anyway, those are my thoughts - for now.