Aside from the visuals effects, I'm also wondering how Kubrick would approach some key themes in the trilogy? One thing that comes to mind -- Tolkein, I think, could be described as a reactionary in literature, who portrayed modernity and industry as pretty much evil.
Well, Tolkien set out quite consciously to write an epic in the old meaning of that word. When you remember that the past is always a Golden Age in epics, sagas, legends and the rest, the aversion to progress and modernity come into focus. He'd been playing around with the languages he'd created, he'd charted them through their various changes, and came up with a rough history to explain how/why those changes occurred that he then spun stories out of.
I'm sure Tolkien's time in the trenches played a part too. He was a Victorian/Edwardian living and writing in a very modern and, to him, a very ugly post-WW1 world.
Kubrick, OTOH, I would describe as an ironist -- a major theme in his work is the machine that works as intended, resulting in (unintended) disaster...
For the reasons you note, the Ring would be Kubrick's focus and the Ring's corrosive effects on all who came into contact with it or lusted after it. This might mean that Kubrick will avoid Jackson's biggest mistake: writing out the Scouring of the Shire.
Let me start by saying Jackson did an excellent job with the films, one that I had frankly thought would be impossible. I can understand why he made the choices and changes he did, except for cutting the fate of the post-Isengard Saruman and the Scouring of the Shire from the narrative. In doing that Jackson reduced the films to just another action-adventure movie, a fantastic action-adventure movie, but one that failed because the menace inherent in the Ring and Sauron's victory was not driven home as was done in the books.
Early in the books, when LOTR still resembles the Hobbit, Sam asks about "what happens next?" listening to someone chant out one of the ancient elven epics. It's all nice and dandy that the dragon was killed, princess rescued, and other heroic feats performed but Sam wants to know what happened after all that stuff. At the end of LOTR, Tolkien gives Sam what he wants while also ramming home the horrible fate which has just been averted.
The readers and the hobbits have been "traveling" through the story as tourists. They've met strange people in strange lands and witnessed strange things. None of it seems real to either the reader or the hobbits because all of it is so out of their experience. The only place the hobbits "understand" is also the only place in Middle Earth which is familiar to the reader; the Shire. Elves, dwarves, and kingdoms of men may have been saved but none of them are as familiar as the Shire so the threat they faced is necessarily diminished.
Tolkien gets all the "important" stuff out of the way a quarter of the way into the final volume. The Ring is destroyed, Sauron reduced to a shade, the King returns, lands and titles granted, and everyone has a good time. Just the thing for the end of our tourists' trip. Right?
Wrong.
When they get back home, the hobbits and the readers finally realize just how bad things could have gone elsewhere. Saruman has set up Mordor Lite in the Shire and all but destroyed the only thing in the story both the hobbits and the reader are most familiar with. Suddenly the menace is presented in terms which the reader can intimately grasp. It isn't about elves, dwarves, and all the rest. It's about people just like the village next door being enslaved while their lands and homes are destroyed. The hobbits fight again, this time for something far more comprehensible, and when they win something comprehensible to the reader is restored.
Contrast that to the ending of Jackson's film which see the four hobbits enjoying a pint while Sam wanders off to get laid.
I'd like to think Kubrick would understand that and would ensure that the story's real ending made it into any film or films he made.