I think that Trek's later showrunners just weren't as science fiction-savvy as they could've been.
I don't disagree with your points. Star Trek could have gone deeper. And you're right, TNG and later shows sort of dropped off the transhumanism elements as a general theme (though specific stories did pop up occasionally). Their focus seemed to move onto other things.
Early TNG experimented with a lot of the wacky stuff that TOS was known for:
You and Christopher make good points. And TMP is my all time favorite Star Trek film--which deals a lot more with pure sci-fi than any other films, including having a human join with a machine.
However I think we have to look at the business end of things as well. As much as I love TMP, I have no illusions that is a common feeling among fans and the general public. TWOK was many times more popular than TMP and that became the model for many of the future films (save for maybe TVH--which also didn't deal with transhumanism so much as ecology).
And the first season of TNG, which seemed to deal with transhumanism a bit more was also generally regarded as one of the poorer seasons of TNG. TNG didn't reach the height of it's popularity until about the 3rd to 4th seasons, by which time the regime had changed largely to the one we are familiar with during the Berman era and they obviously had other priorities.
Now I don't necessarily blame transhumanism for the how season 1 is perceived--that had more to do with specific stories that were just poorly written or executed. But different producers/writers were at the helm by season 3 that just had different stories they wanted to tell and focus on. And as TNG became more popular, like anything in life, you want to continue to do what works.
Perhaps it's a pity they didn't explore transhumanism more during the Berman era...but I still loved all those shows for other reasons. There were some excellent stories and threads during those years that had nothing to do with transhumanism maybe, but were still entertaining for other reasons and sometimes had other meaningful messages they portrayed. And I realize your critiques of those shows doesn't necessarily mean you didn't like those shows. But I look at the whole product. And as a whole I still loved TNG, DS9, Voyager and Enterprise. There are things they could have done better. But the beauty of Star Trek is it's still being made...and it sounds like the current producers are more open to exploring transhumanism nowadays.