Pretty sure relays blowing up didn't take out the star systems they were in. How else would shep be alive on earth after the charon relay blew up? Agreed that is one of the vague/confusing part of the ending though that makes it so icky.
Also, yeah, protheans didn't make the relays. Whoever made the citadel/reapers/etc. made them.
To the topic: destruction.
Losing EDI and the Geth are sad, no doubt, but I couldn't see how my character could make a different decision.
Control sounded horrible because given a few thousand years, who's to say Shepard doesn't end up acting just like this kid? After you have to put down a couple civilizations for the 'good of the galaxy', you are bound to become a bit jaded. If control gave me the option to take control and immediately fly all of the reapers into a star, that'd be different. But it was obvious that wasn't what the choice entailed. It is just delaying the cycle, and slating future civilizations to feel the wrath of the reapers.
Synthesis sounded appealing, it took some time to eliminate it. After a bit of thought, I realized that Shepard had just fought an army of synthesized creatures. That's really what the husks are, right? So what does synthesis look like exactly? Why should I trust this AI again? Am I really in the position to play god and hand down this decision for the galaxy? Yeah, can't see Shepard choosing that option without a lot more faith in the AI than I felt justified, or a clearer view of what the choice entailed. Plus they had just said that organics don't want their form changed. The bit from legion about not giving races technology and abilities they aren't ready for seems pertinent, as well.
So, destruction. Losing the Geth and EDI was horrible, yes. But, it is the only ending where the reapers are gone. The galaxy gets to determine its own fate. I feel like my paragon Shepard would have faith in the galaxy's ability to do that. Shepard would feel guilt over wiping them out, but they did wipe out an entire solar system, too, so such measures are not beyond what the character is capable of. Even if they are paragon.
Plus, the only explanation for other parts of the ending is that Shepard is unraveled, shell-shocked, well beyond their limits, and not necessarily thinking logically. Must. Destroy. Reapers. It is the original mission, after all.