If you're on a branch with one of the main girls, you'll get more time with them, and you've got less options with the other girls. You can flirt pretty heavily with the other girls still, but there's this little counter "tc" (total cheats?) that increments every time you stray, so there's likely to be consequences.
On the others path you can mess around with all the side girls.
Regarding starting a new relationship with the main girls after season 2, not sure, but it always feels like there could be a solo relationship with Josy in the future.
The story feels fairly weighted regardless of which branch you go down. Just be warned, episode 9 is mostly the Halloween party and a few flashback scenes to fill in some details. I got caught off guard when the Halloween party and so did the episode. It was still a decent episode, but not as good as the previous seasons, I feel.
Hoping episode 10 steers it back to awesomeness again. And cheating, lots of cheating.