As far as plot holes go the worst has got to be Star Trek III: The Search For Spock. The plot makes no sense at all -- Kirk's motivations would only make sense if he knew Spock was alive on Genesis and there was a way to restore his katra, but he doesn't.
He's operating on faith--and his final log report from TWOK:
"There are always possibilities, Spock said. And if Genesis is indeed...life from death, I must return to this place again."
The set up and motive was already in place (the belief that Genesis might restore Spock--the reason Spock's tube was aimed at the planet
, rather than anywhere else in space). With that, there's need to question Kirk's resolve after the Sarek conversation in TSFS.