Matt, the way I interpreted it, was that the mass relays just sent out the "effect" you chose. Like if you chose the red it would destroy all reapers in that vicinity. Thats the problem with the ending though, its too ambiguous and leaves everyone wondering what exactly happened.
Check again--the relays blow up when they shoot their neon-colored death across the galaxy.
See at 2:05 to 2:15 or so--pieces of the relay go flying out from the neon-colored death ray explosion:
http://www.youtube.com/watch?v=DPhWndG6EIY
The only difference I know of that's substantial is that in the 'control' ending, the Citadel remains intact (but the Mass Relays still go boom).
Yeah I suppose you could be right. Aside from the endings, this game was probably the most fun i've had playing a game though. I'm excited to see the DLC coming out for it. AS LONG AS ITS FREAKIN FREE. f*ck EA.