Over the years I've heard this more than a few times and it's an empty charge.In retrospect, TMP was perhaps trying too hard to be 2001 instead of, say, Star Trek.
GR and Robert Wise were not trying to emulate 2001. I think they were trying for something other than expected run-and-jump. And like "The Cage" they might have lost a bit of focus. There are some paralels betwwen TMP and 2001, but they're not deliberate.
2001 was about encountering an intelligence unlike anything humanity could imagine. We still can't to some degree because we never get to see those aliens, whether in 2001 or 2010. It was addressing the idea "we are not alone" but in a very WTF manner. There is no real resolution to 2001 because the Discovery goes silent and doesn't report back.
Of course TMP doesn't start from that standpoint. The humanity of TMP certainly knows we are not alone, but they can still encounter unknowns. It doesn't take long for them to understand they are indeed faced with an intelligence only they have no idea what kind of intelligence. They take every step forward with trepidation because they feel they have no common frame of reference to guide them. In the end they are faced with the completely unexpected: an intelligence simply trying to understand its own existence. And it has a skewed conception of what life is. The resolution makes sense in that they are able to answer Vger's question (in a roundabout fashion), and rather than destroy itself or the "infestation of carbon based units" when its preconceptions are challenged...Vger chooses to accept the answers and evolves (although into what who the hell knows?).

The resolution makes sense within the context of the story, but it challenges most audiences expectations because it's not action-y and showy.
The parallel with 2001 is really only in that both films are aiming beyond accepted conventions of big sci-fi spectacles. And they are indeed visual extravaganzas. And they both question the nature of existence albeit in different ways.
Certainly TMP also runs counter to what followed which would be more straightforward action-adventure. Oddly it wouldn't be until TFF that Trek would again try to address a big idea: the nature of God. Sadly it was largely a disappointing effort. TFF is much like "Spock's Brain," a solid SF story idea smothered by too much silliness.