My overriding thought would be, ridiculously convoluted story, which maybe-sorta kinda works by some insane internal logic. More like the author thought X would be cool, with no thought of downstream ramifications to a coherent plot.
If you have never seen this summary of the Metal Gear series, buckle up: https://m.youtube.com/watch?v=aaLiLRVeaZA
If it fits in 6 minutes it's not so convoluted, there's a guy who made a (10 hour?) video trying to explain all the lore and story of Destiny 1 and Destiny 2 (and all their various DLC/paid seasons). And the guy who made this apparently lost interest towards the end of Destiny 2 as a live service game so there's easily another 2-3 hours of content covering the final beats of the story.
https://www.youtube.com/watch?v=zzBmOeYmN_M
But I agree the overall story/timeline of all MGS games taken as a whole is really wild. It's definitely quite something.