I'm glad you enjoyed the game! The sequel (Zen: A Gay Sequel, or ZAGS) is under development now, but has no expected completion date at this time.
I tend to agree about the art... the sprites took a bit longer than expected, and the breaks between them made some of their eye sizes mismatch. But the guys are intended to have more "normal" looking eyes, as opposed to more cartoony eyes, so maybe we tended to much in the other direction.
1) In playthroughs where you don't go to the frat house as much, and therefore don't interact with Elliot as much, you'll get that scene to help establish that Carlos and Elliot are good friends (and that there's maybe a hope of something more, on Carlos' part). It's intended to make the eventual Elliot scene and Carlos' confession seem less abrupt.
2) Nope. Jake is more willing to deal with Nate being Nate because he feels he made a stupid spur-of-the-moment decision and doesn't want to break up without giving things at least a chance. If he agrees to date you, it's more because you've grown close as friends and have gotten there more organically. (There's some more background about him and Nate in one of the companion fics.)
3) I think that's it. ZAGS will have more.
Thanks for the comments and thoughts!