Your choices didn't matter by the end?

I don't like MEHEM. Thematically, it's almost as problematic as the OE.

If I could request my own EC, it would have these elements (High EMS variants only in this description):

(1) The Catalyst would be removed. Instead, we find the information about what each of the ending choices do through a different agent. Possibly another prothean VI, or even better, our own scientists and engineers find things out just in time. If, for reasons of coherence, the Reapers need a controlling agent, it is one we barely, or not at all, interact with before the Crucible affects it.

(2) The role of the Citadel and the Crucible are changed. The Citadel is the power source and connects the Crucible to the relays, the Crucible is the machine that can program the Citadel do to things.

(2a) The decision chamber is removed. No more "shoot the tube to make this machine functional" nonsense. The decisions are implemented by starting up pre-programmed sequences within the Crucible. There are many more options, but the scientists didn't manage to decipher more than these three. The Crucible interface is a part of the Citadel, and there is a Prothean device attached to it left behind by the Prothean scientists who changed the Keeper signal. Shepard can interface with it using the Cipher. 

(3) The purpose of the Reapers as the Catalyst explains it is mentioned as one possible conclusion about what their purpose is, but no compelling conclusion can be drawn from the data available and things remain murky enough that it's clear we need not accept it. When confronted with this purpose, Shepard has several options to reply, partly dependent on how you resolved the geth/quarian conflict. 

(4) The themes of the three choices are maintained, but they're changed to stress their positive aspects and most downsides, apart from the fact that half of the galaxies' civilizations are dead, are removed. In detail (I omit any companion-specific scenes in this description):

(4a) Destroy: This is a classic good ending with conventional themes. If you choose Destroy, the geth are still destroyed (you can't remove that without a thematic overhaul), but you get a happy ending for Shepard with them reuniting with their LI in the ruins of Earth. Scenes of ardent rebuilding follow. Cut to 400 years later. The camera sweeps over a futuristic city, homing in on a statue of Shepard and their LI looking up at the stars. The final scene has a fleet of sleek spaceships leaving the solar system. The camera homes in to a galaxy. Cut.
(4b) Synthesis: this is a "weird" good ending with transhumanist themes. If you choose Synthesis, not all life is changed. Instead, only Shepard is changed and becomes the avatar of Synthesis, able to spread the change to others. How Shepard is shown to do that depends on the P/R score. The Reapers do survive, but they become a remote lifeform occasionally called on for advice but they aren't involved in rebuilding. Epilogue scenes show a city with a crystal-themed architecture, and a human standing near a block of apparent stone, extruding a complicated-looking tool out of her finger into it, after which around it, a building starts building itself apparently out of nothing. Another scene sees a man morphing into a woman. I'm not sure whether nor to put Shepard into the scene.  
(4c) If you choose Control, Shepard does become the Reapers' controlling agent, but with a much more hands-off philosophy. You will get the additional option to make the Reapers just fly away. In that scenario, there are hints of CrutchCricket's Control interpretation. 
 

And I like the dark age because I think it fits ME3's "sacrifice" theme better than the arbitrary "feelz" Mac saddled us with.  We're at war with Space Cthulhu, the masters of mass effect technology, and the tech we are most dependent on was specifically designed for us to be dependent on it.  Ever since Sovereign revealed that detail in ME1, I suspected that the Citadel and/or the relay network would have to be destroyed by the end of the trilogy.  I was completely prepared for that.

You gotta start somewhere though.

If you frame it as "collateral damage" or even just "shit happens" I'm ok-ish (again for lower EMS). But if you frame it as "reject the Reapers' gifts" that's what makes me want to flip something. It's almost as bad as the game's Synthesis.

Again, that's really not as insurmountable as you claim. The only reason it's still a thing is because with Mass Relays it's a problem we've never needed to solve. Now without the relays we do. So solve it we will. Either through a feedback system or through disposable modules that are jettisoned once full.

You don't need the complete loss of the relays for that kind of landscape. Have I ever told you about my age of strife scenario? Basically, after the war, the things that united everyone (common threat, Shepard) are gone and there's plenty of unresolved beef everyone has with each other. Asari hid the beacon, Humans had cerberus, Turians and Salarians had the genophage and bomb, krogan will be blamed for holding out etc.  Everyone has bad blood that will need to be aired. Colonies might want independence (particularly in the Terminus), plenty of strife to go around and lots of little factions vying for power. Hell in Destroy the relays may be out of comission for decades not because they're that badly damaged, but because there's less concentrated effort to get them going due to the the ten way pissing contest, if not outright fighting everyone's involved in.

How can this possibly be worse than Synthesis? breaking the relays makes sense, pumping all that energy through it. Synthesis is "organic energy" nonsense!

And again, even if it's a surmountable problem, it's something that's never been worked on. And I'm sure if anyone broached the subject, they'd "laugh the blue off her *ss" Maybe it's something that can be worked on as a consequence of the loss of the relays, but it's not something they can just Macgyver together because "resources"

Well, I guess they can because that's how Mac gets out of narrative corners he paints himself into

To be fair the OE made it clear that Destroy and loss of the relays had a direct effect. Only after players complaints did they alter it that some how they are able to rebuild them. Control and Synthesis you have the Reapers to rebuild.

And that's pretty much the one part of the original endings I didn't have a problem with.  SO of course the only changed that 

And that's pretty much the one part of the original endings I didn't have a problem with.  SO of course the only changed that 

As a HUGE B5 fan, I often find the similarities between B5 and ME staggering.
There are so many things which look as though they were taken directly from B5, I often wonder if it's homage or copying

Yes changed in responds to fans complaining about it.  You hate it because they changed it but they changed it because fans hated it.