Metal Slug 1 is still the best
Well, out of the original trilogy (MS1, MS2/X, MS3). I haven't played the later ones enough to judge them. You see, MS1 is made like a proper arcade game. First of all, there is not a single dull moment aside that submarine ride in the final mission. Environments always change through the level like from the giant statue head to derelict sub to the village to ship wreckage in the first level. Every setpiece has many details and destructable stuff. The city level has more samey buildings but lets you have fun demolishing them. Bosses do not take that long to defeat. The whole game can be easily beaten 1cc, maybe too easy for some but you can select the level 8 difficulty (i'm talking MVS version) for a more hardcore experience. In fact the game is not about how many coins you throw at it to manage through but about having fun and getting higher scores if you're into the competition.
The second game and X remaster add many more enemy types and have their share of quality levels but on the other hand there is some stuff that drag the overall experience down. First of all some levels are not fun at all. The first level has NO stuff to blow up, except enemies - the backgrounds are completely static. The second level is the worst. Not only it is static too, it has that annoying mummy enemies that are bullet sponges and don't let you just walk past them unlike regular soldiers. Then they can turn you into a mummy too and you start walking much slower. IMO arcade run'n'gun game should not slow you down like that. The later levels are better, blowing up stuff in chinatown is great fun. But then there are two long and boring sections - subway railroad and another one where you walk through long and tedious corridor with martians jumping at you.
Then there's MS3 which IMO very overrated. There are even more new enemies and stuff, branched paths and secret levels. And only one level is actually good - the first one if you do not count the secret underwater section. Almost all the others are made of the boring endless corridor sections like the worst parts of MS2/X. You just walk and walk (or swim or fly), enemies jump at you from all sides, and there is barely any cool destructable stuff from the first game. Zombies are the new mummies - just slow you down and make the gameplay more boring. Bosses have insane amount of HP now making the boss fights much longer and less fun. The shmup sections are the new low. I could barely sit through them. MS3 is not really made like an arcade game, it has the philosophy of a not very good and artifically extended console game. Many like the harder difficulty of MS3 compared to the first game but for me it just stepped into a quarter-muncher territory. 1cc is almost impossble and this is awry for a quality arcade title.
There is one more thing that I prefer about MS1 - its WW2-inspired style without zombies/mummies bullshit (kinda miss martians though). But that's subjective of course and I know many prefer the bigger more colorful enemy roster from the later games.