I feel like all three choices amount to, basically, a slap in the face to every single person that's ever played Mass Effect. Not only that, but the ending is also a franchise-killer. Without the mass relays, all of galactic society is destroyed. Sure, conventional FTL still exists, but IIRC the fastest drives can only take you about a dozen light-years in a day. Three games and thousands of hours of gameplay add up to a gigantic waste of everyone's time. There's no closure, and worst of all, no point.
The entire story of Mass Effect from the very beginning has been about Shepard searching for a way to end the cycle of destruction and forge a new path for the galaxy. The choices that were presented to us at the end ignore the whole point of this story. The Reapers warn Shepard that he's (I know not everyone plays a male, but I don't feel like typing he/she all the time) fighting uselessly against inevitability, but he soldiers on regardless, determined to circumvent the fate the Reapers have laid out for the galaxy and create a new future for everyone.
The solution to fixing the ending is so simple, I don't see how BioWare couldn't have thought of it. This whole time, Shepard has been taking what the Reapers have been telling him and throwing it right back in their faces, refusing them and finding his own way. When the Catalyst presented Shepard with the two options, Shepard should have been able to tell the Catalyst to go frak itself and reprogram the Illusive Man's signal to kill the Reapers, rather than take control of them. He then should have been able to use the Crucible to transmit the signal through the mass relay network and kill every Reaper in the galaxy, without harming the relays themselves. This would leave the galaxy devoid of Reapers, but still able to use the relay network. Now, whether or not Shepard survives this act isn't really important. Sure, I'd prefer that he lived, but I don't mind him being a martyr. I just hate that all of the endings we were given essentially render everything pointless.
And I don't really care if what did happen was just Shepard dreaming, or hallucinating, or whatever. That's even worse than it having actually happened, I think. If you're going to stick everybody with a crap ending that ruins the story, at least have the balls to make it real.