I think we were supposed to see Veronica as happy with Piz. She says so, to Mac. Also we see she is sexually insecure and Piz is letting her gain confidence before they take that step and he joins her in homework and in going to activities. Logan is, first off, by definition (look around) an emotional vampire and Veronica, like Keith, is a stayer, not a runner like Lianne (an unpopular opinion). I think the show tried to break Logan and Veronica up over and over, showing it was a horrible relationship and that fans and the network wouldn't let it go--which I think is why the ratings fell and the show was eventually cancelled. If Logan had disappeared to rehab at the end of season two maybe he could have reappeared in season four as a friend. I suspect that is unpopular.
Also: I like Keith but I think he wasn't the best father during the period of the show, but that it was probably okay.
I think the worst thing that happened to veronica was Logan taking the gun away from her on the roof, if he was concerned he should have talked her down. Being raped with her own taser and then essentially having control taken away again was really the worst outcome. I don't know that she would have shot Cassidy anyway, but it was a moment when she could choose between justice and revenge and Logan made it all about him.
And to all, enjoyed reading this unpopular opinion thread. Unpopular opinions are the best.