Then we see him as first officer...for all of maybe ten minutes. Then Spock comes aboard, and Decker gets booted out of his first officer chair, too!
Actually, that's not correct. Decker was still first-officer after Spock came aboard, as the latter took only the position of science-officer. Although Spock had been Kirk's first-officer for the five-year mission, Decker outranked him by virtue of having the official rank of captain to Spock's commander. Decker's grade-reduction was to be only for the duration of the V'Ger mission.
The key to understanding Decker, IMHO, is to understand that even though he was Captain during the refit, he was still new to the officers and crew he was working with, and as Scotty stated, he was "Untried".
I wouldn't say he was new to the crew. Decker hand-picked most of the
Enterprise personnel himself and worked closely with both Scotty and Uhura throughout the refit. It's not clear how well he knew Sulu, Chekov, or Chapel as their statuses during and after the refit weren't clear. They were aboard by the time Kirk showed up, but they may have been there at his request.
You're right that he was new to the captain's chair, but if we're to use the enthusiasm and energy with which he was involved in the refit as an example, he was clearly dedicated to his job. TMP/
Phase II source materials indicate he was first-officer of the
USS Boston for four years, so he had some command experience from that assignment.
--Sran