Ok, having sat through this completely now, here are my thoughts:
The action scenes are great. Which is understandable considering the director's background. Really, I don't mind the dune buggy scene. It's a well placed action scene and it's fun.
Considering they didn't go LOOKING to interfere with the planet's population, and they were removing the advanced tech (B4) that didn't belong there, I don't see any conflict with the Prime Directive that most people bitch about. It's just a middle aged guy tooling around in his inappropriate vehicle.
I was wrong before, there IS an explanation about the age of Shinzon... and it's also the motivation for him wanting the Picard transfusion. I still don't like the clone thing (more on that later).
I HATE B4 and the death of Data, but I see little maneuvering room on that issue.
Talk talk talk, blah blah blah. Unfortunately, my ideas for what might fix the movie removes a lot of character development and introspection that are the hallmarks of Next Generation Trek. (You could also translate that as boring.)
OH and yes I now see the similarity to Wrath of Khan. Very much so. Villain fixated on hero, big space battle with hide and seek, Spock/Data sacrificing themselves for the greater good. Etc.
If nobody mentioned it, I might have missed it, but I don't think it smacks you in the face (much).
The clones...
That's the real problem here. Sure the movie is too dark and fake-ly edgy, but it's not a deal breaker. What goes wrong is not one but TWO clones. Data/B4, Picard/Shizon. It's forced and feels forced. It's contrived and walks around bare-assedly contrived saying look at my ass-y contrive-ed-ness.
One clone has to go in order to make the film work. B4 is a Trojan Horse for Shizon and the route used for Picard's rescue (the double reverse Trojan Horse with half-twist).
B4's removal means cutting the first action scene (slowing the film more), cutting Picard's capture and rescue (removing a big chunk of the film), and removing the hopeful notes of Data living on in B4 at the end.
On the other hand, Shinzon can be crazy and fixated on Picard without them being clones (SEE also: Khan). Picard struggle with his uniqueness is not developed enough to make the clone scenario interesting. Nurture vs. nature is all they left in, and it feels watered down. (Most importantly I see NO resemblence between the two actors.)
I need to figure out how to explain Shizon's degradation, but it would remove loads of painful exposition from the film and prevent the double-clone crapfest from being so painful.
I might just leave the messed up face thing unexplained with the understanding that it's because he toyed around with that funky radiation.
The deleted scenes: largely unnecessary. I did like the second "rape of Troy", but the footage on the 1-disc edition is really dark and grainy. It seems more interesting and makes her 'psych back' at the end seem more satisfying.
The other ending on the bridge is excellent. The seat-belt gag works well, and IIRC wasn't the 'call the captain by his first name' bit used in the original TNG series? (Can anyone let me know about this? It's really bugging me.)
Anyway, my ideal cut would be the removal of B4 and Data's death. Without reshooting the film, I just can't see that happening. The next best thing is removing the Picard/Shinzon clones. It would speed up the pace and lower the contrived-plot quotient considerably.
(I still need to find out if there is a difference in quality or content of the deleted scenes between the 2 different releases.)
Am I going ahead with an edit? I swore I was retired from doing true fan edits. Pending more details on what else is being worked on, I just may do this since it doesn't look that hard to pull off.