In all honesty I think they kind of dragged the whole Xindy war far too long because it was the strength of the show so they basically milked it for too long because in my view having episodic show, then an arc story don't mix and they missed giving the viewer an answer to the whole temporal cold war and that mysterious guy - just think they had a good story to run with this rather than prolonging the Xindi conflict
I liked the Xindi arc, but I do agree they dragged it out too long. Way too many filler episodes that don't add enough to the mission to justify being full episodes.
Extinction: Species extinct 1,000 years ago. Virus turns other species into their species. Phlox finds cure. Outcome has zero impact on the mission. Archer goes insane and has the retrovirus stored aboard Enterprise while his ship is in a region of space where containment systems could be disrupted and the virus could be released throughout the ship. Good plan.

Rajiin ... molests members of the crew to get bio-readings. Plenty of girl-on-girl action with Hoshi (off camera, sorry guys, you'll just have to use your imagination) and T'Pol.

Exile: While it was nice to see Linda get an A-plot, the story was boring. It lacked real tension and the exiled alien was such an unsympathetic character that Hoshi's departure leaves behind no emotional impact.

North Star: In "The Xindi," Reed raises a concern about taking the word of an unsavory alien who gave Archer info on where he could find a Xindi. Archer crabs at him that time is of the essence and they haven't the luxury to be cautious. So why the heck did Archer take some time off to hang around a western town that doesn't have any useful info on the Xindi and ain't goin' anywhere?

Similitude: This is my favorite ENT episode. I just love it. And yet, I have to admit it doesn't really add anything to the mission. And with apologies to TnT fans, the writers could have set up the scene in Harbinger some other way where T'Pol finally gives in to her lust for Tucker.
Doctor's Orders: Love Phlox. But this was pure filler, not to mention plagiarism.
Hatchery: The only thing the NX-01 got out of this episode that proved useful was an insectoid shuttle. That could have been achieved during a reconnaissance mission.
E2: With apologies to TnT fans, I believe this episode would have brought more value to the arc if the crew/descendants had survived and joined the armada to stop deployment of the weapon in "Countdown," and then returned to Earth with the NX-01.