Jak II was always my favourite. Heavily down to the atmosphere of the city, the feel of zoomers and the incredible cutscene animation and dialogue.
Jak 3 still has a lot going for it though.
I think that the gameplay is affected somewhat by "open world syndrome." There's so much to do, like shooting, driving, platforming, hoverboard, dark jak, mini-games etc. that none of these things is honed to the degree it could have been.
Compare that with Crash's refined platforming (esp. Crash 2) or the amazing feel of CTR and its boost system. They had the whole of development to iterate on those core mechanics.