I think they would have ended up together again at some point in the future, when exactly is debatable. I think both were still in love with each other but they felt they should be apart, though maybe for different reasons. For me, Marissa knows she loves him and she wants him but she also wants to find out who she is, outside of Ryan (and also Newport) and hence the desire to get out of town. By comparison, near the end of season 3, Ryan loves her but I think for Ryan there's a conflict of loving her and then not wanting to want her. In some ways this is true also for Marissa but more strongly for Ryan. There is a sense in 3.25, that he's very sure of his feelings again but I think that's more of a function of the writer's foreknowledge that these are some of their final scenes. If you are more in keeping with the selection of episodes after their break-up in season 3, then I don't think they would have got back together very quickly because there was somewhat of a wariness to do so from both parties.

As for season 4, yeah I remain annoyed how they handled everything. Marissa's death became a question of revenge and a device for overcoming his saviour complex (and I have so many issues on that saviour thing but I won't get into it). The fact he loved her was kind of treated as a footnote. There are some scenes where it shines through the driving arc is built on a theme of revenge and guilt when really the crux of it is the simple pain of losing someone you love. Julie's arc is the most moving for me because it's so honest and raw. One of the Ryan scenes which I really do love in season 4 is when he's at her grave waiting for Julie. For a brief moment, the camera pans to his face and his pain is palpable. That's what is moving, the stuff afterwards that he realised he has to kill Volchok, I couldn't care less for. (Talking about that scene, I have to say nothing gets me like Julie saying 'I'm here everyday'.)