Ah. I'm certainly not going to say the movie was a brilliant work in terms of plot. I do, however, have a few comments in response to your own.
[spoiler]
Puritan wrote:We know why the geostigma is there, but the idea isn't elaborated on. How do so many people have the disease and why is it feared? We never see it as more than a rash, so it hardly seems like the scourge it is made out to be.
It seems to me that the movie implies that the geostigma causes pain (notice how often Cloud winces and holds his arm) and eventually death (given the statements Tifa makes to Cloud regarding it). At least I assumed as much, because if it's just a fever it isn't very impressive.
Puritan wrote:Secondly, they bring up ShinRa and intimate that they may be trying to continue their old research, but this storyline isn't pursued any further than simply having them recover JENOVA's head.
I got the sense that they weren't continuing their research so much as attempting to clear Shinra's name by doing good for the planet. But we all know the real point of this plotline is to instigate the main story involving Jenova.
Puritan wrote:Thirdly, the film goes out of its way to bring up characters and locations in the film, but it never explains why.
Does it need to? This is obviously a fan film, not a work meant to stand on its own. They threw in a lot of unnecessary places and characters just for the sake of the diehard fans who want to see them again. I agree it is a weakness, but I think it is within the character of the movie.
Related to this, however, is my biggest problem with the movie: Cloud does
everything. I've said this before, so I won't belabor the point. But it seems to me that other characters should get to accomplish things as well, especially because all of their fans will want to see them in action.
Personally (as if anyone cares), I would have had the ending be a bit more complicated, with a variety of fights going on in a number of places with different objectives. Cloud would chase Kadaj, Vincent would fight Yazoo, someone else would fight Loz, and everyone else would fight Bahamut Sin. In the end, of course, it would still come down to Cloud versus Sephiroth, but I think it would be more interesting in the process.[/spoiler]