I can see the reasons for wanting Big Boss over Snake, since Snake's story has ended with MGS4 and the spotlight has been on Big Boss for a while now.
Still, I think Snake should stay the way he is.
Maybe he could have alternate costumes based off Big Boss' outfits from Portable Ops and Peace Walker in addition to costumes based on Solid Snake's outfits from MGS1 and MGS4.
Solid Snake in Brawl is like a composite character who takes elements from both himself and Big Boss, but... I think having Big Boss' facial appearance and costumes could be confusing since the two are separate characters...
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I do think however, that a new Metal Gear stage should be from MGS3: Snake Eater, because it would represent Big Boss' saga, much like SSBB's Shadow Moses stage represents Solid Snake's saga. And there's also the 3D port of Snake Eater which was an Nintendo-exclusive.
I actually posted an idea for a stage on the old closed social thread a while back.
http://smashboards.com/threads/super-smash-bros-4-wii-u-3ds-topic.324221/page-1134#post-15754961
It'd be set on Groznyj Grad, it would be more actiony than Shadow Moses, and integrate SSB's fighting with Metal Gear's stealth system.
Hazards would be from Big Boss' games, and would include the AI Weapons from Peace Walker, Metal Gear ZEKE, One of the two Metal Gears from Portable Ops, (can't decide which) and of course, the Shagohod.
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