^I guess the other factor is that he wasn't really part of the chain of command during the films like he'd been during the TV series. He was second-officer during the five-year mission but didn't seem to have any responsibilities outside of engineering during the films.
There wasn't a need for Scotty to be in command during TMP, as Kirk, Decker, and Spock (and perhaps Sulu) would have commanded the ship before he would have. In TWOK and TSFS, Kirk defers to Saavik (for teaching purposes) and Sulu (in Spock's absence), so there's no reason for him to take the conn in either of those situations. By the time TUC rolled around, Chekov had risen to second-officer, so Scotty wasn't needed then, either.