The original Metal Slug has a very interesting development history. Back in 2014, two French guys met some of the Nazca developers behind the original MS as well as its spiritual predecessors (Gunforce 2 and In The Hunt) and produced two videos about the development of those games, featuring even original production art.
I posted the details on TV Tropes a few months back but I don't think they're still very well known (and some of my recollection of the video was wrong OxO) so I'll repost the summary here for the sake of discussion.
-The first iteration of MS was played with the tank. There was no pedestrian gameplay and Marco and Tarma did not exist at this point.
-The tone was more somber and lacked any humour, being more in line with the team's previous post-apocalyptic games at Irem.
-The backgrounds were redrawn. For example, the entire first stage, and not just the second half, was set inside a swamp.
-The game was much shorter: Stage 2 did not have an equivalent in the original version ("Metal Slug Zero" was supposed to have 6 levels like the final one, but the Kobe earthquake prevented one of the designer from coming over), and levels were shorter and simpler (for example, level 3 did not have the climbing portion or a mid-boss battle). The game was lengthened after SNK refused the original build, the developers reasoning being that since the Neo Geo was also sold as an home system, the game should be of reasonable length.
-The original plot was that General Morden had spent years planning a coup and managed to conquer all of the worlds major cities in his opening salvo, helped by the horiffic tactic of using POWs as human shields. The original player character, Phil John, was an engineer for the Regular Army who was working on the Metal Slug prototype, and took it with him to join the resistance. Player 2 was a gold Metal Slug piloted by one named Michiko Nakajima.
-The bearded POWs originally were blue pallete swaps of the enemy soldiers. Furthermore, instead of giving items, rescued PO Ws would either climb to the top of the Metal Slug and fire their bazooka, or stay next to it and throw grenades.
-Speaking of the POWs, apparently all of them were named after real POWs 0_0
-The prototype was completed and demo'ed at SNK's Osaka location 1995. While it was well-received by outlets like Gamest, neo geo fans and SNK itself didn't care much for it, saying it felt too short and subdued, that it didn't have the "fun spirit" of a Neo Geo game. After this, the developers went back to the drawing board and conceived the green trooper enemy, a development that set the direction of the final game.
-The video also reveals that rearranged themes from Metal Slug 1 were composed for X and are still present in the ROM, that an "X" version of Metal Slug 3 was planned, and that the antagonists of Metal Slug 4 would have been fish-people (as hinted in the ending of Metal Slug 3).
-Nazca was always a SNK joint: they were set up to port SNK's games to the Saturn and Playstation. They insisted to be able to make an original arcade game. SNK allowed them to make it on their off-time.
-The developers categorically deny the popular rumour Irem employees went to work to Aicom and made Pulstar as a successor to R-Type. Infact, they didn't care much for that game, perceiving it more as a "rip-off" than an "hommage" to their work on R-Type.
-The developers also deny Dolphin Blue (another run & gun game for the Atomiswave) was intented as a spiritual successor to MS' saying "only two MS developers worked on it" and that it was "a complete coincidence".
-The random UFOs that can appear in Stage 3 and Stage 6 were random details the main graphic artist added because he thought "it was neat" and they were not setting up for the sequels, as some thought.
-SNK didn't have faith in the game and didn't produce a lot of home cartridges as a result. The success of the game was a surprise for everyone involved.
The video ends with the two guys teasing they may have found a lead on a prototype cartridge, but whatever they found is "sleepy" and it won't be until a long time. There's been no news since then.