I don't mind the Season 3 storyline for Trip and T'Pol. I think it was a good setup for a Season 4 where they would attempt to forge a romantic relationship (whether it was derailed or whatever). And though I can see arguments for and against the lovemaking in "Harbinger," I had no problem with the "morning after" scene. To me, T'Pol looked to me as if she was backpedaling because she didn't know how to handle the emotions she had unleashed (sorry,
JiNX, I'm one of
those posters

), and I like how Trip handled it--not stalking away in a snit but choosing to be patient with her (because she was worth it). The episodes after that were a bit pushme-pullyou, but the two seemed on solid ground by "Zero Hour."
The characters seemed pretty much in character (to me) until "Daedalus." What we saw in "Home" (mutual affection, Trip's sacrifice and desire to support T'Pol) and "The Augments" (she missed his friendship) didn't seem consistent with the now-free-of-Koss T'Pol telling Trip in "Daedalus" that she needed time
alone 
to work out her identity crisis.
Even if one rationalized that T'Pol swung the pendulum too far the other way and tried to be an uber-Vulcan, it didn't seem in character for her to shut Trip out completely, which she seemed to do after "Kir'Shara." I agree that the damage she suffered from the trellium could easily have been brought up as the reason for her mood shifts, whether she confessed to Trip (or even Archer, who was friend to them both), or it came up in conversation with Phlox. But that storyline was tossed after the presto-change-o T'Pau mind-meld in "Kir'Shara."
Then Trip
runs away to
Columbia, which (to me) seemed out of character for him. I wish there had been a more substantial reason for him to leave than his inability to cope emotionally with a relationship that was on the skids. One would think that a guy who stood by supportively as the woman he loved married another man would be emotionally tough enough to deal with being on the same ship as his lost love. (At least, the romantic in me wanted to see that.)
If Hernandez had asked to borrow Trip to help get
Columbia launched, and that's why he left--and then the bond manifested itself, and T'Pol got a clue and realized she needed to find a balance between her new Vulcan identity and the post-trellium emotions she now had to incorporate into her life... I think that might have been a compelling way to take the storyline. There would still have been plenty of fodder for conflict (necessary for drama), without that soap opera vibe.
There was good material in scenes like "The Augments" Romeo & Juliet talk, and the one between Trip and Phlox in "The Aenar" where Trip is trying to figure out how to deal with his feelings about T'Pol, and the quiet little talks between T'Pol and Phlox about her emotional struggles. In a different context--with the characters staying true to what was set up in "E2" about T'Pol's emotions, and in "Home" regarding Trip's desire to be a supportive presence--I think such scenes would have been great ways to illustrate two people trying to cope with the circumstances (Koss, trellium) that had pulled them apart against their will.
Instead, they took turns bailing on each other.

It just didn't feel right to me.
There was potential for a very interesting Season 4 T/T arc, quietly running parallel to the "A" storylines that TPTB were doing to try to keep the show alive. If someone had worked out a season-long story arc for them, properly structured, and nurtured it...but I think the writers were juggling too many plates, and this was a plate that got dropped. They got the relationship back on track by "Terra Prime," which was a good setup for a Season 5 storyline, where they would
really attempt to forge a romantic relationship...

Ah well.