It's smart for them to protect their IP. Regardless of how good a fan thing might be, it's in their interest to be the sole provider of their IP, so as not to cheapen the value of their own stuff.
I'm sure there's alternatives, but it's not their obligation to seek those out to be nice.
It's cold, but important. Things like the Nintendo PlayStation and the Phillips CD-i were pulled out of for this same objection to lack of control of their own content. The latter they weren't able to get out of completely, and we have memes forever to commemorate it.
I'm not saying AM2R is Wand of Gamelot.
I am saying that their is little incentive for Nintendo to have fans give Metroid away for free when they're trying to sell it.
It's why Steve Jobs killed off 3rd party Macs when he returned to Apple. Don't let anyone outdo with your own stuff, or worse, make you look bad.
I personally would like them to hire that fan though, as AM2R was one my favorite games I played last year. Or at least cut some kind of deal or good will pact. Like when that guy was hosting NSMB Wii roms before the game out, and they cut the lawsuit and gave him free crap.
So Reggie didn't say it the best way to please the GAF crowd, but he's making the correct move. Or at least what is arguably the correct business move.
I want better than this, but I don't expect it.
They're not sega.