I expect Buddy to have been neutralised, and possibly Vinny taken out along with him - Buddy is almost entirely a problem for Quinn, and secondarily Riona, only impinging on Tremolo if the player picks one of them to pursue.
Vinny is much more of a personal antagonist for Tremolo - he's an ex-DIK, closely tied to Nick, and Tremolo has, literally and figuratively, taken his place in the DIK mansion, living in his library, and serving as heir apparent to the frat's leadership. He's a strong antagonist, but he's not quite final boss material - it'd be a little disappointing if it turns out he's been swept aside by Quinn's drug strike, but it wouldn't derail the rest of the game's plots. Most damningly, he has no real connection to any of the main girls except through Tremolo.
Stephen has something in common with Patrick - Maya's dad - he's at the heart of the problems for one or two of the main girls (Sage and possibly Bella) and resolving the situation with him will probably take a chunk of an episode, but he's not really a direct problem for Tremolo. Stephen's got a lot more connections than Patrick did, with links through Quinn and the "scholarship program" to Maya (and through Maya to Josy) and, of course, his role in Mona's departure also ties into that. And, of course, his interest in Bella gives her a stake in settling him beyond her friendship with Jade and Cathy. Overall, though, his role is largely as Sage's problem.
Magnar is a mastermind villain - he thinks he's Lex Luthor, but I agree with the comparison to Littlefinger - the success of his scheming relies on no-one realising he's behind it. He doesn't offer a very compelling confrontation, but he does have connections and impact all over the place - the Cathy cluck impacted Bella, Jill and the DIKs; the frat wars he stokes impact the HOTs, DIKs, Alphas, and Jill; he's tied into the game's economy for Seasons 1 and 2, and it turns out he's linked to the Brawler minigame - he's tied into so much, and he's at the same level as Tremolo and most of the other characters, unlike Vinny, who's playing by entirely different rules of engagement, or Stephen and Buddy who are operating at a higher level.
For a physical final boss, Caleb makes a lot of sense - from the start he's been the Alphas' dark reflection of Tremolo - the freshman pledge taking on a leadership role after excelling at things the frat values - the one strike against him (and it's a significant one) is that he's only really a nemesis for Tremolo, and even there it's not that personal.
My guess is:
- Buddy is already dealt with.
- Stephen is going to be an anticlimax and never really confronted directly.
- Vinny is going to shoot Tremolo (non-fatally), serving as a cliff-hanger, and get his ass dragged away by the cops.
- Magnar and Caleb combined are going to serve as the final boss: Magnar being defeated by bringing the frats together and comparing notes, but Caleb refusing to buy into Tremolo's story.