Damn this is going to be a hard one. Metal Gear Solid V is easily one of the greatest stealth games ever created, I don't know if I'll ever really play a stealth game again on the level of Metal Gear Solid V, but the story (or massive lack of one) is an issue. I can't really put MGSV above Spiderman simply based on Spiderman very much is a complete title in regards to having a solid story, solid gameplay and of great quality.
If Metal Gear Solid V's story could be done based on what Kojima wanted vs Konami, I think ultimately V's story would have been just as good as the other MGS titles, but it feels like Konami doesn't really want to really have a game where you play the "bad guy" and it seems like Kojima had to write around a publisher that simply wants some of theses characters almost flawless. So if we simply got a story about Big Boss starting Outer Haven and Sons of Big Boss being born at the ending etc, I don't think many would be so upset, it simply feels like a Metal Gear Solid game in gameplay only and the story is like....."other" lol.
Its in my top 5 favorite games this generation, but if I have to go part by part, element by element, I can't really put MGSV above Spiderman, as I liked all elements of Spiderman, I simply can't say the same for Metal Gear Solid V.