TMP is superior to every Trek film made after TUC, including the Abrams films.
I believe the reason so many take issue with the film, whether consciously or otherwise, is because it's not a conventional adventure in the sense that Star Wars or the later Trek films was. The core narrative is about exploration and discovery, both without (V'ger) and within (V'ger, Kirk, Spock, Decker, and Ilia's journeys) and this is pure science fiction.
We start the film learning that Kirk is incomplete without his friends and command, that Spock is incomplete with his humanity and his friends, and that Decker and Ilia are incomplete without each other. We learn all of this before the Enterprise even leaves dry dock.
We then learn that V'ger is also incomplete; it's searching for its Creator, for a sense of purpose and belonging.
In the course of helping V'ger find the Creator, Kirk, Spock, Decker, and Ilia find what they're missing. The resolution of the film is that these characters are all made whole and, as a byproduct, Earth is saved from destruction. The film ends with Kirk, Spock, and McCoy reunited with the rest of the crew and the Enterprise heading out to continue "the human adventure."
This story requires the audience to think, to feel, and to even look within to fully appreciate the narrative resolution. As a result, TMP was always fighting an uphill battle, as the film that led to its creation as a motion picture required little thinking (I say this as a big fan of the original Star Wars films) and the films that followed in both general science fiction and sci-fi and Trek in particular required less thinking and introspection. They were compelling, engaging, moving, and yes, even thoughtful, but they don't work on the same level that TMP did.
I believe the same holds true to a lesser extent for TSFS and TVH. Consider that TSFS has been considered "proof" of the "Odd number Trek movie rule" despite being a film that requires the audience to face grief and sorrow head on. There is no easy way out for Kirk and his crew, and Kirk loses more than anyone else: his ship, his son, and his future in Starfleet. TVH, meanwhile, asks the audience to consider complex ideas like the value of pain and how humans use it or avoid it and how the drive for knowledge of the divine can be both positive and incredibly destructive.
In contrast, the TNG films don't take any time to plumb any real depths, instead sacrificing narrative logic and established characterization for boring and uninspiring action set pieces and attempts at "humor" that are more embarrassing than funny.
TOS is my favorite Trek series, and that includes the films, but as much as I enjoy them, I feel it's a shame that all of the films after TMP ignore its existence and that TUC ignores the events of TFF. Say what you will about Roddenberry and Shatner, but both wanted stories that put exploration and narrative depth before action. Their films weren't retreads of TOS episodes, they were revisiting the spirit of exploration and human self-discovery present in a series that most moviegoers likely hadn't watched in its entirely before heading to the movie theater.