"Honestly now, if you were in the game industry and were offered to make a Metal Gear game, would you turn it down, especially if it was one of your all-time favorite games?"
Make a NEW game from an existing franchise? Yes. Remake an existing one? No unless it was a big change like taking an old NES game and making it 3D. But that's just my opinion and I'm sure other people would think differently.
The SK/Metal Gear example isn't that great because SK seems to be really excited about working on the project. Still you have to wonder why Miyamoto offered the project to SK. A game that already has the story written and the whole basic gameplay scenario worked out doesn't need the expertise of a company like SK to work on it.
I think the "problem" is more with Nintendo spreading out the Mario franchise to every developer they work with instead of encouraging them to work on something new. Sonic is Sega's most popular franchise but you usually don't see any Sonic games being made by anyone but Sonic Team. Each team does it's own thing and as a result Sega's games have a lot more variety than Nintendo's. There's no reason why EAD, Intelligent Systems, Camelot, Hudson Soft, and Treasure should all be working on Mario related games. If EAD can't handle Mario on their own then don't make as many Mario games.