The problem with that particular flavor of cerebral  storytelling is that it often doesn't make for good movie making. Don't  get me wrong, I'm all 
for high-concept sci-fi, exploration of the unknown, but for every 2001,  there's five of "Sphere" or "Mission to Mars." TMP lands somewhere in  between. The parts where 
it "explored the unknown" were alright, but then it went into "V'ger  Existential Crisis" mode like it just read Nietzsche for the first time,  and it was downhill from 
there.
Ultimately, I feel that style of storytelling is better suited for  television. The characters should be the ultimate focus in a movie, and  they weren't in TMP.
(More on topic, no, I don't think WoK is overrated.)
		
		
	 
Although I don't agree, I guess that you're right as my taste, but first   and foremost motivations tend to diverge to the point of being almost   veritably unique, especially when it concerns cult films as well as  even  lesser known movies (adhering to movies that are even more rare  and/or  overlooked than the films you see being appreciated in different  cult  and nische groups).
After practically being born as a cinema buff having seen all the great   classics of Kurosawa, Bergman, Hitchcock, Johm Ford, James Whale etc.,   the latest years I've discovered more and more what a weird (almost to   cretinous levels) and abstract conceptualist I am, even in many areas   outside of film. Antinomical to when I was 12-15, I've found myself   overlooking or even caring very little for how character-driven   something is nowadays. The importance of it depends on what kind of   movie it is and what the ambitions or general idea of the creator seems   to be. For me, opulent conceptuality can sometimes override and   remunerate for a lot of other flaws in a film. In some movies, it's the   only thing that matters. When I praise a Lucio Fulci film, I rarely   praise the sometimes sleazy feel of the movies nor the zombies and the   blood 'n' guts in his most famous films. For me, the most interesting   aspect is the eye penetration and blinding as the most powerful of many   symbols representing oppression which is the most central theme of   L'aldila (The Beyond) or the stylish intro scene delineating death of   art. Or the attack on catholicism in Beatrice Cenci and Non si sevizia   un paperino which got him blacklisted.
And sometimes it's neither as "pretentious" or nebulous like those   examples. Sometimes, the concept of Style-over-substance can be enough,   meaning story being subdued for the film to only be meant as an visual   experience of puissant cinematography. I don't really qualify that as   exploitation, which I hate, because in exploitation there are no real   concepts nor real ambitions in collation to many other films where there   is traces of fat and limpid concepts no matter how single and  uniformal  they are.
Even though I hate inconsistencies in Star Trek (I thought 
pon farr   was something deeply private, Mr. Spock!), I think it's one of those   culture phenomenons where in the end one of the biggest things about it   is the rich conceptuality and prevalence of Hard Science Fiction. I   think TMP were more successful in that area while WOK tend to be a more   collatively straight-forward story. I also thought that the faster pace   made it feel less like Star Trek and more like an epic war drama in   space. I guess that basically, it comes down to which episodes I liked   the most and what aspects of them and other episodes I appreciated the   most. 
Even though I love Khan, and the epic atmosphere, cinematography,   direction and performances in WOK, I find that the purpose and   background of Khan's activites to be too linear and straight-forward   (damn how I hate to repeat that word, especially considering WOK is not   at all so straight-forward compared to many modern blockbusters) to   really be interesting in more ways than one. The basic plot is for me   the biggest obstacle, even if the script and everything else is   exceptionally good. Even if I still want Khan, I'd prefer another plot.   And if I can't have Khan then I'd rather see a new Dr. Korby or Dr.   Adams whose work has evolved to much greater extents than their   predecessors' or the return of Charlie who's intent on claiming the   world that rejected him and his superior powers as his own. I know   everyone would hate these premises, but for me those themes feels more   Star Trek to me than simply a baddie wanting to avenge the death of his   love.
And like I said, I do not at all dislike Wrath of Khan. I just like TMP a   little more and here I've tried to sum up why and explain that even   though I like them almost equally, it is for totally different reasons.   Wrath of Khan is easier to appreciate for the experience and adventure.  
EDIT: When I think about it you're probably right in that TPM would be better off as an episode.