Again, if you want superherohype to vote on the "greatest movies of all time" that's one thing. But, a quick search has no credible critic calling TDK one of the greatest movies of all time. (Heck, it didn't even beat out Twilight at the MTV awards.) There was an outcry, certainly, but I say that much of that was from the TDK geek crowd and a sizable portion outside that were basically playing the "it would be good for the Oscars to nominate a movie as popular as TDK", not many critics were calling TDK one of the all time snubs. Certainly there's zero evidence that even a minority would put TDK in the top 50 all time, much less most. At the very least, it hasn't passed the test of time. Nor, has it given birth, nor is it likely, to any influential movement like French New Wave, Italian Neo-Realism, German Expressionism, etc. I don't know if I'd even call it as influential as The Matrix, which certainly has influenced 21st century action films. Other than more films being shot in IMAX, which TDK wasn't even the first at, what's TDK's influence likely to be?
Heck, I suspect Heat and Blade Runner, which are significant influences on TDK, would outpoll TDK among critics.
FWIW, I really don't object to it being on the list. It's high on IMDB's site and that's probably more representative of the average reader here. But, I really doubt that TDK would do all that well among acadamia and critics.
The Sight and Sound polls that are done at the beginning of the decade are pretty much the definitive critics poll. Does TDK really look like it would fit in with those choices. See
http://www.bfi.org.uk/sightandsound/topten/