*Shrug* A lot of both the complaints and suggested improvements seem nitpicky.
I think with the Ba'ku being on the planet for only (?) 300 years, before the Federation existed (that could have been made clearer), the Federation still come off as invaders much more than the Ba'ku come off as squatters (with a whole uninhabited planet/region, let alone before the territory owner did own the territory, the analogy seems really silly). In the film the Federation still seem like owning the planet only in the sense that it's within their territory because they defeated some other entity for vast amounts of territory including it later. Although I also don't see how with just one village of 600 the Ba'ku should have, or even really do claim, the whole planet.
Deep Space Nine crossovers could or could not work better than what we did get (although the opening diplomacy scene is pretty bad, overly goofy even just in terms of the film itself). Directly dealing with the Dominion War, and wanting to get advanced weapons for it, could be fine, better, but it could also make it feel too much like plot and themes of another series. The film does already believably somewhat reflect the Dominion War, a reason why the Federation needs the medicine improvement, without focusing on it a lot (and a lot of viewers do still sympathize more and side with the Dougherty over Enterprise crew view anyway which is OK).
Edit: I think the film could have used less humor, and/or less broad slapstick humor (although I usually like slapstick humor) without going as grim dark intense war drama, or even intense war drama all around the main plot, as some people seem to want it to have gone. And I do like that the Federation wanting to use the resource to help a lot more people is still a compelling, tempting dilemma rather than more clearly in the wrong like wanting better weapons even if you do need them.