Well...first, I have yet to have the "hindsight is golden" experience of finding The Motion Picture great...I suspect that's because--as I discussed elsewhere--having stood in line for hours to see it opening night, it was a crushing disappointment...no matter what hindsight did to improve it, it couldn't overcome that feeling. I suspect Wrath of Khan got made because a) Paramount listened to the reaction of the fans and realized there was a huge fan base but they had completely misread what was wanted and b) fans among the writing/tv community came forward and said "this can be done much better"...so they gave it a second chance. The movie franchise exists because Wrath of Khan succeeeded where The Motion Picture didn't: it generated repeat visits by the core fans.
Movies used to need that, and as fans we used to do that. I saw Star Wars 13 times in 35mm and 4 in 70mm on it's initial release (and I was a slaggart...true fans make me look like I didn't even like the thing).
I was forced to see The Motion Picture a second time in a theater (long story) but Wrath of Khan I happily saw 10 times.
Second, I think it's natural to have doubts...in fact, it's probably healthy.
Thanks to Ron Salon for the signature banner!