Karathos said:
While I'm not saying it's necessarily good writing to leave your audience to fill in the blanks for themselves, I would like to offer up some points.
As for "the destroy all synthetics negates the other two options" argument, I don't see how it does. Maybe it would if you were offered two choices, but you're not: you're only offered one. The reason it's the "Renegade" option is because you make the decision that synthetic life is not worthy of saving and as such can easily be sacrificed to spare organics...even if the eventuality exists that more synthetic life will some day rise up.
I believe the reason the "take control of the Reapers" ending is the "Paragon" ending because in that case, the Reaper's still exist...and so does Shepard in some manner of being. This means that the Reapers could be repurposed and become benevoent machines that would help rebuild the galaxy since it is now Shepard's will that drives them.
Considering the effects of each ending, there's no way Shepard was walking out of there alive. He/she either dives into a massive energy beam and disintegrates, grabs a hold of two electrodes that rip his/her consciousness out of his/her body and makes him/her the new will of the Reapers, or he/she sets off some sort of specialized EMP that wipes out all synthetic life...and considering the fact that Shepard's only alive thanks to synthetic parts, this means that he/she would did as well.
As for the destruction of the relays, it was established from ME 1 that the Citadel was the heart of the relay network, having absolute control over it. As such it's not that big of a stretch to assume that it's capable of firing out a beam that could bounce and filter its way through the entire network. As for the relays' destruction causing the destruction of every star system that had a relay, one possibility is that the vast majority of the incalculable energy within the relays is absorbed by the beam before it fires off to the next relay, leaving the destruction of the relays to be far less devastating than what is seen in Arrival in which you use brute force to destroy one by slamming an asteroid into it.

All this said, I will easily give you the major plothole of your final squad being back on the Normandy...last I recall, they were right behind you when you're making the charge for the beam. The only possible way I can try to spin this one is to say that we don't know how long Shepard was unconcious after taking a Reaper beam to the face. When he/she wakes up, though, we do hear a voice on the radio say that the entire force that made the final push had been utterly devastated. To that end, it can loosely be assumed that perhaps your squad pulled out (though I agree that this itself is highly unlikely given their commitment to Shepard and the mission) and retreated back to the Normandy.
In the end it, like everything else, all comes down to each player's individual opinion. I do feel like the endings could have been better, but I'm fine with them as they are, so I won't be joining the ME 3 Rage Association any time soon. Can't remember if I mentioned it in this topic or another one, but I got my ending "experience" during the segment when you're in the last human outpost, about to make the final push, and you speak with all your squadmates one last time on your way to the strategy meeting with Anderson. During those conversations, I was nearly moved to tears...mostly because of an overwhelming emotional response to the thought of "Holy shit...this is really it...I've heard a lot of bad stuff about the ending to this game...but for better or for worse: this is it. This will be the end to the most amazing videogame series I've had the privelege to play." So I guess if anything, I fall into the ranks of the "It's not the destination, but ratherr the experience of the journey" camp. Because no matter what you think of the ending, surely we can ALL agree that god
DAMN this has been one hell of a journey!