I think Black Mesa has better potential as a stage, plus it's probably more iconic in context with the Half-Life series. Pretty much the only thing Nintendo would need to change with Black Mesa is to remove the blood and the like, and I think that's a compromise I am certain all Half-Life fans would accept.
While I am posting, I wanna bring up a small wishlist of music tracks from the Half-Life series that I would love to see in Smash would Gordon make it, remixed or otherwise.
Hazardous Environments (duh)
Adrenaline Horror
Military Precision
Nuclear Missile Jam
Diabolical Adrenaline Guitar
Closing Theme / Tracking Device (Natural choice for Gordon's Classic Mode run credits song)
Alien Forces (Note: Since Gearbox made Opposing Force, I don't know if Valve actually has the rights to the soundtrack. I am assuming they do, however. I think I will ask Gabe Newell about it)
Vortal Combat
Last Legs
Half-Life is definitely no slouch when it comes to great music!