Cogenitor gave them a perfect reason to back away from the close friendship, and I'm not sure they ever saw a good reason to go back to it. After all, by this time TPTB had already established that Archer was the driving force in the Federation. In season 4 he would become the savior of the Vulcans. I almost think they wanted to create a lone wolf, a towering historical figure who would be worthy to be the idol of James Kirk. Towering figures don't need anybody, including sociable engineers. Unfortuantely, the Archer we saw on screen desperately needed Trip, or someone like him, to keep him connected to the world around him.
I think the way the show was set up was a perfect example of faulty thinking. You create a ship full of the best of the best -- Hoshi, Trip, Malcolm, T'Pol are all trailblazers in their given areas -- but then to decide that only one person, Archer, is ever going to amount to anything. If all you want is Archer the Great, why not put him on a ship with a bunch of mediocre gofers and be done with it.
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