Absolutely it is.
I think this thread proves it. There is unrequited obsession with it among Trekkies. I have no idea where it comes from--I can only guess it has something to do with the nostalgia goggles.
Fans act like it's one of the greatest films ever, and it simply isn't. It isn't even one of the greatest SF&F films of all time. I could easily name 20-25 genre films I would put before it just off the top of my head--even ones I don't like.
The single biggest problem with it is breaks so many of the most basic rule of story telling.
The most significant of these no-nos is "show don't tell." Every major plot-point (specifically those that directly related to the antagonist) occurred off-screen. The audience was then introduced to them later via exposition. Your first grade teacher told you not to do that. The rule still applies to hack directors.
Secondly, all three climaxes were resolved with some kind of deus ex machina. It's really hard to take your heroes seriously if they can pull rabbits out of their hats on a whim. Obviously, this has become a major point of contention with the later Trek series and a valid critique. My only question is: why does TWOK get a free pass?
It introduces a completely pointless subplot: The Genesis device. On the surface, it served three purposes: moved the plot along, was an outlet for Khan's revenge (see above), and was a set-up for the next film. On the other hand, it added nothing to the main plot and theme. In fact, I would only argue it handicapped the movie.
Don't believe me? Imagine for a seconded the whole Genesis bit was completely omitted from the film. Or if that's too much, pretend the Marcuses are still just in phase one of the project. Now go through all the major moments of the story and think of all the different ways things could have been advanced. Khan's revenge suddenly becomes so much more poignant and focused, and the story isn't stumbling over itself to fit this cumbersome gizmo in somewhere.
As for it being there to set-up the next film, that's just another one of those silly no-nos. Think of all the great duo/trilogies. The first story is either completely stand alone or the stories are completely connected. The ones that try to dangle strings generally just fall off the radar. This, for example, is why the Donner Cut of Supes II works so much better for a lot of people.
Now I admit this film does have its merits. Montablan's performance, while not great, is at least very entertaining (as Dennis and teacake have pointed out) and probably worth the price of admission.
The ending is also very touching despite being stunt theatrics that are completely askew from the rest of the plot.
But the problems are just too glaring. They drag it down from would could of potentially been a great film to just an average space adventure.
Is it the best Star Trek film? Well I suppose that could be argued. (I would say no.) But that really isn't saying much. Despite the fan fair, Trek films pretty much range from mediocre at best to abysmal at worst.
That's not to say I don't enjoy them. I can sit down and enjoy any of the eleven. But I don't have any false perception as to where they rank in the annals of cinema.
