After two serious cliffhangers in the first 2 seasons, I don't mind not having a third.
We have the set up for the kidney transplant in next season. Although we see some healing between Hope and Maura, we also see no improvement between Maura and her sister since they are still hiding Maura's involvement in the transplant.
Interesting to me, we also see a very vocal opinion from Jane on the subject and I expect to see that opposition continue next season. Maura has admitted she's too nice and always does "what's right" which Jane is well aware of and so tries to protect Maura from herself.
I also really hope we see Maura's FATHER next season. I really loved it when she protested Hope's description of Paddy as her father. I think its high time for us to see her adoptive father, and I can't think of a better time for him to show up than just as she's about to go under the knife.
I also was surprised that Frost, of all people, admitted to having a crush on Jane. (I really thought it was their other partner Korshak (?) who was crushing on BOTH Rizzoli women.