I actually like the basic plot that the novel writers came up with for
The Good That Men Do--Trip being recruited by Section 31 to infiltrate Romulan space and sabotage their Warp Seven program--and in a Season Five that ignores TATV I'd still like to see that idea, minus the whole part about Trip's death being faked. Instead I'd say he willingly went along with it because Elizabeth's death has driven a wedge between him and T'Pol, and by doing this he can get away for a while and figure things out. I imagine it being a season-long storyline (combining the events of
Kobayashi Maru), with Trip returning to
Enterprise at the end of Season Five as the Romulan War officially begins. He and T'Pol reconcile when he returns, of course.
And maybe while Trip is gone, Shran can take over as Chief Engineer, and constantly complain about how slow and primitive the pinkskins' engines are.
I'd also liked to have seen more of Reed's own history with Section 31, maybe an episode where Harris informs Reed that an old partner of his (whom he'd thought was dead) was now working for the Romulans, and Reed going off to stop him, perhaps with Hoshi in tow.
Another idea I had was an episode set on the nearly-completed Starbase One, where Archer and the crew are touring the facility, which is hijacked by Orions (working for the Romulans), who threaten to blow up the station if Starfleet doesn't relinquish its claim on the star system, which is conveniently close to Romulan territory. Archer, T'Pol, and company have to free themselves and fight their way through the Orions to stop the station from being destroyed.
Essentially, Season Five should have been about building up the tension between Earth and Romulus, with Starfleet working feverishly to shore up its fleet (both building new ships and upgrading old ones), and Archer and the
Enterprise crew continuing to patch up old grudges between the disparate members of the Coalition in order to present a united front against the Romulans.