They wouldn't, outside of diehard fans. He'll probably stick with the main story points established in MGS1, and then branch out from there with his more familiar tropes and ideas. I don't think that "Dirty Duck" would resonate well with today's gamers in any context. And again, the 8 bit games were done well before Kojima had solidified his creative formula.
I could see the Metal Gear 1 & 2 remake being done in a similar vein to the recent Mortal Kombat remake a couple of years ago, where Netherealm basically retold the first 3 MK games through the story mode.
He would split the 2 games into separate acts, similar to MGS2 and 3, with Metal Gear 2's backstory being the meat of the plot. Big Boss and Grey Fox would be the main villains, and would be backed with a new team of meta operatives in the tradition of FOX-HOUND, Dead Cell, Cobra, etc.. Instead of the Metal Gears being 2 separate models in the first and second game, it would instead follow along a similar narrative path as the Shagohod in MGS3, where Solid Snake damages it in his first encounter in Outer Heaven, and later destroys it outright by the end of the game in Zanzibar, or Outer Heaven 2.0.
