I actually finally got around to watching JoJo (at least I did a couple of weeks ago), and I have no idea what I was missing.
I've seen the four parts of the anime that are currently out and kinda spoiled myself on the other four parts (which is fine cuz I'll probably forget what I know by the time they get animated).
My favorite part would either be 3 or 4, although I do like 1 quite a bit too. Part 2 was decent, but the first few episodes/chapters left some things to be desired.
My favorite JoJo is actually Jonathan. Part of it is because we share a first name, part of it is how although we saw him for only 8-9 episodes, we got to see the majority of his life onscreen, and I find him relatable to a certain extent, especially early on.
And my favorite non-JoJo character is either Polnareff or Kishibe.