In my opinion the Twin Snakes was not a very good take on the original.
It's like with the first 3 games, they make another version of the original games, that while having graphics misses many vital gameplay and cinematic things.
For the NES Metal Gears, they just can't compare to the MSG games. The MSX games seemed to do everything so much better.
For Twin Snakes you could argue the graphics and gameplay are better (even though the models don't look anywhere near as good as they do on PS2). But I don't think you could ever say that about the cinematics… ever. Snake does not use swords, they aren't his style, and he isn't a ninja! Not even close!
It would have required a remake, not a remaster. An remaking a game like MGS1 would take a lot of time and money that they probably wouldn't see again until MGSV is out.
Peace Walker would be easier for them to port, and people were probably irritated that the most recent game, with such a major influence on the series' plot was not available for people with consoles (MGS1 is), so by making an HD version of PW, that would mean so much more to them.
EDIT: BTW, Darkstar Twin Snakes was NOT made by Kojima and his team… explains why it missed the mark… the first 3 MG games were always remade by another team onto a Nintendo console… too bad you can never find a Nintendo version and say it IS better.