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.
Kirk simply broke Vulcan tradition by a) shooting Spock's dead body into space and b) not returning his katra. Sarek wanted to bury Spock at home and store his katra somewhere.
They never intended to put Spock's katra back into his body.
The intended to get Spock's dead body (the USS Grissom had reported the finding of the torpedo) and then get McCoy to Vulcan. They were just really lucky that they found Spock alive, and then attempted a different
Vulcan procedure that hadn't been performed for centuries.
Kirk also never thought Genesis would revive Spock. He simply started to think positively. Spock died, and an entire new world was born at the same time. He was just being sentimental in his log entry.