I think you guys are looking at it the wrong way. SSBB is not giving free advertising to MGS4, MGS4 is giving free advertising to SSBB!
PlayStations are known for having Metal Gear games, it's what they do. That's a FACT. Nintendo's are NOT known for having Metal Gear games (unless your are old school). If you go up to someone and say, "Have you checked out that Metal Gear game for that Nintendo system? It's awsome!", they will respond, "Oh, you meant to say either PlayStation or PlayStation 2. Clearly you did not mean to say 'Nintendo', as my in-brain Googleing of '+Nintendo +Metal_Gear -Twin_Snakes' turned up 0 results".
The only think that might happen is that ads for MGS4 will give some free exposure to SSBB, but more likely they won't effect each other very much.
As for Kojima's evil Nintendo comments, I think It's a simple matter of putting Business Sense before personal endeavors. If a game company was pitching an idea to Nintendo, "This game will be the next unholy union of Goldeneye, Halo, Tribes 2, and WoW in multilayer awsomeocity, and here is PROOF, you cannot fail and will make trillions of dollars." Nintendo is not going to say, "Yeah, well you called us 'Poopie heads' 5 years ago, and now you want us to mutually benefit each other? Go away, good luck finding a publisher who wants to make money".
A good business person isn't going to care about some guy calling it's product a lunch box. All that matters is what ends up on retail shelves (or rather what flies off retail shelves after marketing). If a picture of snake on the box helps sell 1,000 more copies of SSBB, it will be worth it.