Even from the first season on, Joey had a more honest relationship with Pacey then she ever did with Dawson. She could never tell D how she felt, even though it was obvious to everyone around them and he was amazingly obtuse. But with Pacey she could joke, be a smart ass, cut loose. The scene where they are collecting snails, after Pacey's ill fated menage a snail, is indicative of who she is despite Dawson. I think that she fell for D because she didn't know any better. Joey lived a pretty insulated life, the same small town, the same people. Pacey did too, but even though he was small town in body, he was not in spirit. He fostered growth in everyone around him and I think that this is what made Joey fall for him. As she said in True Love (not verbatim by any means), everyone tried to hold her back but not him. He challenged her, made her world bigger just by being in it. P showed her what love is supposed to feel like.