From a character perspective, Beckett seems less fun these days. In series 1 she was cautious about castle, in series 2 she was far more playful and toyed with him. Now she seems rather clinically written and they tend to leave the jokes to castle, esposito and ryan. She still has her moments I guess. Maybe the show is becoming less appealing and I'm just trying to find reasons for it.
Her being shot, flatlining, and being brought back, along with her dealing with her own mortality as well as the accompanying PTSD from being shot might have a little bit to do with it. Added into that, she's feeling her way along about Castle's revelation that he loves her, and her wanting him to but still being afraid to let her walls down. Doesn't really lend itself to playfulness and toying with an object of affection.