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LeVar Burton says he's deeply conflicted about the new "Star Trek" movie ... telling TMZ there's something missing from the flick ... something extremely important.

Burton -- who famously starred in "Star Trek: The Next Generation" from 1987 to 1994 -- says he's already seen J.J. Abrams' "Star Trek Into Darkness" TWO TIMES ... but that doesn't mean he approves.

"At the end of the movie, I really care about what happens to the characters ... but I'm pretty much missing Gene Roddenberry in J.J.'s interpretation ... and at the end of the day, that's just not OK for me."

For all you non-Trekkies out there ... Gene created "Star Trek" back in the '60s and was heavily involved in the storytelling until his death in 1991.