I got to some of the nitpicks with the script (I read really slow!). He is incorrect about two of the plot holes, and misses a few huge ones:
1 So, if I'm understanding this right, the Head-Staplers wanted to be off the planet, but once they got what they wanted, they decided to get revenge. Just read that again and realize how stupid this plot truly is. This film didn't need a rewrite; it needed a bullet between the eyes.
2 So, just because some of the younger Villagers dared to be curious about the outside world, they were forever exiled from the planet? Given that living on the planet means eternal youth, this seems pretty harsh. Couldn't they have just split into a separate colony elsewhere on the same planet? This doesn't make the "good guys" look particularly sympathetic.
3 If they're all the same race, it makes even less sense that it takes "ten years" for the Head-Staplers to experience the effects of the planet. Especially since the effect on humans (and Klingons) is almost instantaneous. (I guess you could argue that the planet has an instant effect on androids, too, but I'm inclined to think that's just Data being an idiot.) The "can't share the planet" argument, which basically drives the whole story, has now become so hopelessly convoluted that there's no possible way for this movie to come to a satisfying resolution.
For 1 & 2, the Son'a were curious about the outside world, but were exiled for trying to take over the colony. They wanted revenge because their goal was to break the villager's isolationism - not leave the planet. While I agree that this plot point is poorly developed, and not very well spelled out, he misses the whole point.
Second, the biggest plot flaw I found was the idea that the Prime Directive should apply to worlds within Federation space occupied by races that have knowledge of the greater universe. In the series, we've seen that the Federation has absolutely no trouble forcibly relocating colonists when treaties change political realties - like with the Cardassians and the Maquis. This situation, while not entirely similar, wasn't a whole hell of a lot different either. The Federation we know and love would have absolutely no problems with moving in, saying "this is our space. Get the fuck out!".
Second, the idea that within 100 years the exiles from a colony of only 300 or so people could grow into a "race" powerful enough to subjugate two other races is rather implausible. Even allowing for reproduction, there would have been only a few dozen adult Son'a, tops. Not enough to operate a fleet of starships.
Both these plot holes could have easily been avoided by having the planet be outside Federation space, not a subject of Federation laws, and with a much, much higher population. Granted, it wouldn't be a tiny village, and there would have had to of been more than one holo-ship, and the special effects budget would have been higher - but the story would have been better!
Another issue - The Son'a could have easily gone in and wiped out the Bak'u at any point. The whole idea that they needed the Federation because the planet is in Federation space is laughable, considering the Federation had never heard of the Son'a or the Bak'u previous to this incident. The Briar Patch was obviously of little interest to the Feds, so the Son'a could easily have gone in and wiped out the colony, did their thing to the planet's rings, or simply settled on the planet, without a soul noticing.
