I agree with all you said. I would add that Susan Sulivan as Castle's mom is another standout supporting character.Alexis' dorm is close by; I feel she'll still be a part of the show. She has always been my favorite teenage character since the show first started, and Rick Castle has been a great father to her. I think and hope the show is too smart to lose her permanently. Their separation scenes as she moves to grown daughter touched my heart. There is so much love and respect in that family that you almost never see on tv anymore.
I agree that they are handling Beckett and Castle's new relationship with tenderness and humor. I'm sure we'll see some ups and downs, but I think the glue is there to hold them together. Ryan, Esposito, and Lanie are among the best written and acted supporting characters I've seen. The appeal of the show would be lessened without any of them.
I knew from the moment they found that doll in the storage bin that it would be the key to solving the crime. That was confirmed when it was shown to be something that brought out a softer side of Gates (who is still the weakest character for me.) There was another clue later on when someone, I think it was the rich woman whodunit, said something about when she saw the doll was missing....
I adore this show, but still want to see some more of the poker games.