Yeah, and the writers of Star Trek (2009) have admitted TWOK is basically the Holy Grail of movies for them. I think they were influenced greatly by TWOK in their writing. There are some points you made that I hadn't picked up on too. Now, I don't think all of it was intentional but I do think it played into their thought process. Ditto for STID (some of which was overt--like the whole death scene, but in reverse, I'm sure they thought they were being cute there but I was just like OMG, seriously, and then the Khan scream

).
And again, there's a lot I liked about Star Trek (2009), the whole it's not a pure reboot, but different universe sort of thing I thought was a different avenue to take. It allowed them to 'reboot' Star Trek to allow them freedom to tell new stories, but it didn't trash everything that came before. And I liked a lot about STID too. I was glad Beyond finally seemed to break the cycle. There was a revenge element to Krall, but I don't honestly see a lot of TWOK parallels with Beyond (and there were nods to a number of Star Trek films in Beyond).
I still think it's a stretch to be comparing 2009 to TWOK though. 2009, was a fresh, original take on Trek (hence it's good box office showing), there's very little here that feels lifted from other Trek outings IMO other than the odd nod or homage.
STID obviously is a more contentious outing, but as the film is effectively an alternate universe take on 'Space Seed' featuring the aforementioned villain, comparisons to TWOK are going to be unavoidable. That being said I thought the reverse death scene, and Spock scream was a step too far for me, but ultimately, it's a couple of minutes screen time out of a 2 hour + movie, so it gets a pass from me, the rest of the film is it's own thing, and is a damn enjoyable blockbuster.
You can't say the same about Nemesis though. That film has several quite large plot points that appear to be almost flat out copied from TWOK, from the weapon having 'the ability to consume organic material at the subatomic level' - spoken by Crusher, which is very similar to some the dialogue in Kirk's quarters in TWOK, data planting his 'Katra' in B-4, ship battle in a nebula where communications are lost, to the villain setting off the weapon in a final suicide bid, to data's sacrifice. The film positively
reeks of it desperately wanting to be TNG's TWOK.
Yet I still love the film. I think the visual effects are largely excellent, and clearly the best in the TNG series, the Enterprise E never looked and moved as good as it did in this movie, and the ship battle I still find to be thrilling all these years on, and the desperation at the end on both sides makes for an exciting finale to the film, despite it being heavily influenced from TWOK. Some of the sets fell a bit flat though, especially on the Scimitar, where it all looked a bit cheap and bland in places, still 60 million ain't a fat lot of cash for a major sci fi film made in 2002 so corners had to be cut somewhere. At least the FX wasn't the horror show that TFF was.
Data's death scene could and should have been much better, but I think the scenes afterwards on the bridge and in Picard's quarters make up for it, and it brings a tear to my eye still.
Same goes for the wedding - a lot of people here deride this scene but Picard's 'family' part of his speech always makes me feel emotional.
I found the score to be superb also, way better than Insurrection, and easily on a par with First Contact.
Being a big fan of Tom Hardy, I always enjoyed his performance in this, but the 17 hour wait in orbit when he needed Picard's blood was lame and unnecessary. A lot of people also slate his motivations for attacking earth, but I was always fine with them, he is much more powerful with the backing of the Romulan military (who let's not forget were goading him to attack earth) than he would be alone, and would have become the leader of the most powerful empire in the quadrant had his plan come off, still, his character could have been written better.
Other things that needed rethinking for me was finding bits of B-4 around the planet which was just contrived nonsense, the buggy scene in general, the Reman boarding scene (just turn the fucking lights up!) and the fight with Riker was piss-poor too.
I really appreciated the darker, more adult tone of the film too, again, I can see they were going for a harder edge with this (like TWOK surprise, surprise) but it works for me, especially after the lame humour and awful, pretentious Baku from the previous movie.
Overall I find the positives outweigh the negatives for me, and I'll rewatch this film at least once or twice a year, whereas I just don't the other three TNG films. It's just a good sci-fi action romp with some of the best starship porn in the whole series. I know I'm kinda wrong, and anyone who actually says to me they think it's garbage - I won't really disagree too much, but I just really enjoy this movie.