This is certainly a good idea, but I have three reasons why it shouldn't be implemented:
1) Smeggs reason above, this really fucks over anyone who DIDN'T pick the destroy option.
2) I think BioWare chose this ending specifically to avoid having a "manly space marine run in guns blazing and having a cigar on a pile of dead Reapers" ending, and have something a bit more thoughtful and reflective. Whether or not that was the right move, or whether the ending was thoughtful and reflective, is a matter of opinion (despite what some people on these forums may have you believe), but if that was the reason they did an ending as crazy as this, I think their decision to end on a non-guns-and-ammo note should be respected. Hell, blasting the Reapers manually using the Crucible tracks awfully close to the last bit of Halo Reach.
3) While I'm personally fine with BioWare tacking on a bit more to the end of ME3, they should ABSOLUTELY NOT pick a fan-made ending. Now, this is not meant as an insult to you, OP, but I think that using fan-made endings would be very disrespectful to BioWare's immensly talented writing staff if, should a new/improved ending be written, they are completely circumvented by a fan-made ending and end up not being able to finish a series that they've all put their heart and soul into. Not to mention that using fan-ideas sets a bad precedent - if game companies could just use fans to write their stories, then they wouldn't bother hiring paid writers, and lots of talented people could be out of work. Not that I'm saying all fan-ideas are crap, but letting the fans decide the integral backbone of a plot is bound to backfire for somebody.