I doubt Logan was ever an exciting boyfriend. He always seemed to be their for sex, and to get help (find Mom, why is money leaking out of my trust fund, I'm accused of murder again), otherwise doing any recreational activities with Dick and similar buddies, and presumably later with the Navy guys, too. I doubt he'd spent as much as a year with Veronica since the end of the movie and books. Deployment, training, dropping in unexpectedly. I mean, he probably came back for spring break to see Dick, right, more communication with the bro than Veronica? He didn't share his life with Veronica and was manifestly barely able to stand listening to her tedious and disagreeable complaints about Neptune and cringed whenever she asked anything of him. I mean therapy, realistically, would have only made them aware of how much contempt he had for her at this point and how little hope their relationship had of succeeding. I think she knew it, too, which is why she rejected the idea of therapy.
I mean both of them were doing the best they could, and Logan was trying to force the life he had always wanted, but there wasn't any soulmate between them. In canon.
Veronica probably would have been happier to have someone who spent time with her and might even help raise the kids. Duncan could have been that, but potentially Piz would have worked. Or someone totally different.