It was instead developed first for the MSX, and the fact it had to be ported over to the NES is something that makes the series’ creator, Hideo Kojima, very unhappy.
In an interview with Nintendo Power, Kojima goes to town on the game and the team responsible:
I had absolutely no participation in the development of the NES version. The NES version was a pitiful title developed cheaply and simply by a small team in Tokyo. That was during the bubble economy where anything and everything that was released would sell. I came across the game in a bargain bin and tried play it, but the game design is pretty bad. There is some gameplay that includes infiltrating a base that didn’t exist in the original. However, even I, the developer of the original game, was unable to infiltrate the base even once.
Furthermore, being Metal Gear, it goes without saying that Metal Gear should make an appearance at the end. However, from what I’ve heard, due to the technically difficulties in displaying the sprite on the screen, they swapped Metal Gear out for a gigantic monitor. That made me see that whoever created the game had no sliver of appreciation for the players. However, even thought it was an abomination, it was during the bubble economy and it sold millions overseas. That title has only soiled my reputation.
He’s no doubt just upset the NES version couldn’t include the 39 hours of confusing chit-chat he originally had planned for the game.