I agree with a lot of that, but I disagree that Nemesis didn't have a message of its own, namely that of nature vs. nurture, what forms a person's character, etc. (B4 vs. Data, Shinzon vs. Picard, both superficially similar, etc.)
Indeed. NEM had one of the strongest, clearest philosophical throughlines of any Trek movie, which is why I think it works so well as a
Star Trek story. It's a classic Trekkian exploration of the human condition and its betterment: are we damned by our nature or do we have the power to choose to make ourselves something greater? Not many Trek films have such a strong philosophical core. Let's see:
TMP: Broadly about the search for our meaning and purpose in life, and the idea that it takes emotion to give life meaning and enable us to grow.
TWOK: Some stuff here and there about coping with mortality. Largely about stuff blowing up.
TSFS: Uhh, friendship is good? And more stuff blows up.
TVH: Save the whales.
TFF: The main philosophical thread seems to be about accepting our pain as a learning experience rather than denying it by embracing false prophets and easy answers. Surprisingly, one of the clearest philosophical threads in the Trek movies, though not developed extensively or very cohesively.
TUC: Largely a topical, political theme about accepting change and not being afraid to let go of old hatreds.
GEN: Similar to TWOK, an exploration of fearing mortality vs. accepting it.
FC: Uhh, obsession is bad?
INS: Learn to stop and smell the roses.
NEM: Would we be the same people if we'd been raised differently? How much of our essence is intrinsic and immutable? Does our past limit who and what we can be, or can we transcend it?
ST'09: Friendship is good. And stuff blows up.
So not really a lot of deep philosophical themes in the Trek movies. Which isn't necessarily a criticism; a lot of stories are more about character or plot than theme. TWOK and ST'09 are light on theme but are acclaimed for their character studies.
The films that are most driven by philosophical questions are TMP, NEM, and to some extent TFF. INS tries to be a thoughtful, introspective story, but the script they ended up with didn't have a particularly strong driving idea. TVH and TUC have topical messages, but they're more concrete, social and political ideas than abstract philosophy.
And NEM's exploration of its philosophical question is perhaps the most intensive of any of the films, as it drives both of the core conflicts and is examined in practically every scene between Picard and Shinzon. NEM is also the only Trek film where there's such a strong, nuanced personal connection between the captain and the antagonist, so that focuses it even more.