I certainly think an argument can be made that Nemesis had greater similarities to TWOK than both Star Trek (2009) and STID. Jaime had some interesting points (some of which I didn't even pick up on). I think what I saw in all 3 films that was pulled from TWOK is the whole villain has a revenge grudge and wants to destroy Earth with a weapon of mass destruction. It was the major plot point that after I saw STID I thought, I hope in the next film we can at least have a villain with different motivations. Beyond had a little of that too, but Krall's motivations were a bit different, and the rest of the movie was pretty far removed from TWOK (plus, I was just so happy that Earth was not involved at all I probably would have forgiven almost any oversight--even the stupid Sabotage scene).
But yeah, while I don't think the film is above criticisms, it really just comes down to the simple I liked more than I disliked. And yeah, I think there were little bits that had they been developed better this could have been a blockbuster film. There were little nuggets that I wish they had developed further. Like his motivations for destroying Earth--he basically wanted to prove to himself and everyone else that while he appeared human, he was nothing like them--that was poorly developed. And I too thought Hardy made a good villain (I compared him to Luckinbill's Sybok--while I didn't care for Sybok being some never before seen brother of Spock, I couldn't knock Luckinbill's performance--ditto for Tom Hardy).
And I dare to say the final battle was probably the best of the movies. Star Trek (2009) had the Enterprise battling the Narada, but Abrams constantly shaking camera and excessive lens flares pretty much washed everything out (I swear I was getting motion sickness), STID was a little better but was brief and the Enterprise was greatly outgunned by the Vengeance until the torpedoes were used (though I was glad that like Nemesis, they decided to add a debris field between the ships--always amazed they forget that little detail). Beyond's space battles with the swarm were interesting, but not really comparable. But Nemesis had a sustained battle between two somewhat comparable ships (the Scimitar had their cloak but the Enterprise wasn't without it's own teeth, and the ramming scene is one of my favorites of the films).
I see it like I do the Bond films - they've pretty much all got some villain looking for world domination or whatever, but I don't see those being accused of copying what came before, it's just kind of expected from the franchise, Trek films get slated for it because of it's extensive TV history, where Earth-attacking villains were pretty thin on the ground by and large and a multitude of other themes were (rightly) explored. I expect the stakes to be raised considerably when I watch a Trek movie (otherwise what's the point), which is why I generally regard Insurrection and, especially The Final Frontier to be the worst films in the franchise.
Regardless of how you view the objective quality of Nemesis, you can't deny at least it felt like the stakes were high, the crew were at serious risk - there's a major character's death and on first viewing it really felt like they were fucked and had no way of getting out of the situation after the desperate ramming sequence. Bar the Riker fight, I think the third act of Nemesis rocks. It felt very much like the end of The Wrath of Khan to me, which was obviously deliberate. Unoriginal yes, but exciting and entertaining nonetheless.