The actual mechs are just mcguffins in every single game. You can substitute them for any action movie plot driver (super virus, NOC list, secret computer program, nuclear bombs etc) and they all still function just fine with minimal modification. The plot to MGS1 isn't actually superior because you're chasing down a robot, the plot to MGS3 isn't improved by the Shagohod being a robot. By the time you get to MGS4 and 5 the mechs have almost nothing to do with the story. It's just a plot about AI's controlling the world and vocal cord parasites. They contain mechs because the series is called "Metal Gear", and that's about it.
You probably have to have Rex in MGS1 because of the series namesake, but the Shagohod is actually a detriment to MGS3.
Clones shit is bad and has always been bad. I don't even want to talk about the silliness of Liquid Ocelot in the sequels. If you were making a one shot movie of MGS1, you could quite happily just make Liquid and Solid the literal children of Big Boss.
But there's a question you have to ask, which is whether you're trying to make a good movie, or whether you're trying to be faithful to the series, because those are pretty much at loggerheads with one another. There's so much camp on every level of MGS, even in the "relatively grounded" first game. Psycho Mantis, Decoy Octopus, Revolver Ocelott, Sniper Wolf and Vulcan Raven would all need to be toned down if you were trying to make it "serious" as opposed to just some sort of comedy. Even Kingsmen is about 10x more serious than a straight adaptation of MGS1 would be.
