Money > whatever personal **** you're talking about. Not to mention, well, they've treated even other high-end (ex-)personnel similarly. They're draconian ******** to a 't.'
I should also mention that Metal Gear also isn't legally Kojima's IP. It hasn't been for a looooooooong time. Konami can do whatever the hell they want with the property/licenses and Kojima can't legally lift a finger to stop it.
And you think Snake doesn't have precedent?
Smooth Criminal
That's not the case if you look at their recent track record of business decisions. It's like Konami is doing everything they can to steer away from money. You and I may see that Snake in Smash = easy money and free advertising, doesn't necessarily mean they will see that.
I know Metal Gear isn't owned by Kojima, but as I've been saying, that's part of the problem here - if it were up to him, he probably would have been in on launch day. But Kojima wants Snake in the game, so that gives Konami a reason not to do it.
Snake has precedent especially since he is a veteran, but he is a special case in that he is not at all in the right circumstances. The future of his own franchise is even uncertain and looking pretty bleak, and he's in the worst hands. I legitimately think we'd see Disney let Sora into Smash before we see Konami let Snake return, and that's saying a lot.
Either way there is no point debating this because it's not like I don't want him in the game, I actually want him a lot (Snake was the reason I got into Smash). I just don't think it's gonna happen this time. I'd love to be wrong, but I won't be convinced he can make it back, until he actually does make it back.