I really liked most ofl the MGS games, even 2 and 4. I really thought the twists in 2 were cool when it came out. And for the most part the story in that was intelligible.
I also really liked 4 at the time, but I deadass have no idea what was happening in that game. I can remember a ton of cool set pieces, but never why anyone was doing anything. MGS5 is similar, so many different, interconnected organizations with dumb names.