I used to think that all conspiracy theories in stories / secrets / mysteries should be resolved by the end of story, but as time passed, I realized that the best thing about them is when they continue to make people talk about them, and discuss them even years after.
It's kinda like that saying: The point of a horror isn't to explain anything, it is to scare the shit out of you."
- I still remember the time before MGS4 was released, people wanted so many answers after MGS2, some of which were answered in MGS3 in some way, but it still wasn't enough.
There were countless theories on forums, discussions, explanations, such as characters representing the chess pieces...
So, MGS4 happened, is explained a lot of things, for better or worse, we got our closure to the whole Patriots thing, but, at what cost?
Don't get me wrong, I liked a lot of that stuff, but at the same time it killed a lot of magic of simply not knowing everything.