Very well said.
For me, the water plot element was never even close to a deal breaker either. People ridicule it, but the fact is, you could explain that away pretty easily. Maybe they had no idea they were badly damaged by water upon arrival. Maybe by the point they realized it, they still had the hubris to think they could take the resources they wanted from earth before the weakness was widely known.
Regardless, you also make a great point about the "twist." Yes, the thesis certainly seems to involve the old adage that everything happens for a reason- there is meaning in things that appear to have no significance at all. The problem is that the wife's death doesn't really fit that notion, despite it being so integral to Gibson's arc. She basically foretells the confrontation with the aliens and provides the basis for Joaquin (and Breslin by extension) saving their lives. Yet it just did not feel organic. Oh, she had to die so she could have a vision of aliens and how Phoenix could defeat them??
Still, I think it is hands down one of his best films. Though the payoff of that theme does not really work out, I love that scene where Gibson and Phoenix talk about the two types of people- those who have faith and those that believe they are alone. Really solid work their from the actors and well written material from Night himself.
The movie gets a ton of mileage out of the performances, as Gibson, Phoenix, Breslin, Culkin kill it. Also, it's one of Shyamalan's technically best constructed films. Great tension building and execution overall. I'd go higher- probably 7.5 but also have it at the 3 spot for sure.