What makes II, III, VI and VI so special is that they dared to move the characters, and in doing so, dared to move us. TMP said "here's a space cloud looking for God," and V said "here's a crazy Vulcan looking for God," and then basically simply had the characters along for the ride. These would have made great themes for Star Trek episodes, but they don't hold up as being movies.
You're making a false correlation between the plot and the characterization. TMP could have been much more character driven had the filmmaker's chosen to do so, and without hanging the plot. They already had Spock confront his lifelong ambition of total logic and find it lacking. That's daring to move the characters. In TMP's case they just didn't focus on it as much as perhaps they should have. The could just as well have had a character arc for Kirk in which his actions re V'ger force him to confront things about himself. It's not an either-or.