Metal Gear fans know of this title, but most players who started the series with the PlayStation title Metal Gear Solid still don't know that Hideo Kojima's Metal Gear series saw its first console debut back on the Nintendo Family Computer back in in 1987.
The NES title features many of the stealth mechanics that would make the series famous in the games that came after it. The game is also canonical with this title and its sequel fitting in between The Phantom Pain and Metal Gear Solid.
While we can't be certain why this game didn't make the cut, chances are that Konami had some say in what made - and didn't make - the cut to the NES Classic Edition. Considering their poor relationship with Kojima, chances are the game was withheld for legal reasons.