I ignored most of those repeat missions. It turns out pretty much all of them are optional, because in order to trigger the endgame missions you need to recapture the kids and those missions pop up based doing a set number of ANY missions, including side ops(?). So basically you're killing time until the next recapture mission pops up and then once you get them all you get "A Quiet Exit" and "The man who sold the wolrd" endgame missions, IIRC. PW did something similar but that only happened during the epilogue chapter after you'd already beaten like 95% of the story and destroyed Peace Walker. The remaining plot missions were pretty much there just to give you something to do if you wanted to keep playing, but you also had to do them to unlock the ZEKE boss battle which truly ends the story and sets up Ground Zeros(Because it explains how Paz ended up at Not-GITMO).I was on the section where you’re basically replaying earlier missions with more difficulty and struggled to stay invested. Might do it someday but the whole ranking system doesn’t work well in open world sandboxing anyways, since to get the coveted S rank you’re locked out of the fun stuff and stuck with tranq darts and sleeping grenades. Or smoke grenades if you really want to live dangerously.
IIRC Kojima said it was the MGS he always wanted to make but couldn’t due to lagging technology, but it definitely lost something in the pursuit of all that freedom.
Also, apparently you can S rank like half the missions by unlocking the mini-mechs/walker gears and using them to speed to the objective to get record time. I never did it but I've seen videos of people doing it. It does suck that doing stuff the fun way and the "optimal" way are two totally different types of playing, because the S ranks are almost completely dependent on speedrunning.