Most hate the pulley system.
^ Bingo. I strongly dislike the pulley system. I also can't think of anything that PB4 does better than 3. I think the art and music are both better in 3. The fight intros in story mode are fucking awesome. Speaking of which, I finally got a reasonably priced copy of 3 and it arrived today:
(previously played the N64 port a lot)
PB1 - I'm most nostalgic of this one. I also enjoy the simplicity of the single-player. The music in VS mode is so bad that it's basically unplayable though.
PB2 - I don't like the art direction Taito went with this one, but it's otherwise the superior to the 1st game in basically every way.
Ugh, can't say which is my favorite...