While much has been said on the subject of ME3's ending over the years, I do have my own opinion on how to mildly improve it — building on the Catalyst's comments about the Crucible — without damaging the core of Bioware's intentions too much. (Despite any issues I may have with some of them...)
See, the Catalyst talks about how the Crucible is mostly complete/intact, and then goes on to talk about how the Destroy ending will have so much collateral damage. So, my proposal for an improved ending goes somewhat like this:
First, leave the current endings in situ.
Second, add a War Asset to New Game+ for completing each ending with a sufficiently high EMS. Something like this:
Control Ending: Advanced Reaper Identification (Military Strength: 600). ‘Our scientists have decoded details from the Mars Archives data regarding Reaper communication protocols. This has made it easier to track and target Reaper forces’
Destroy Ending: Focussed Energy Arrays (Military Strength: 600). ‘Our scientists have decoded details from the Mars Archives data regarding energy weapon calibration. This has allowed us to tighten our weapons' tolerances, allowing for more damage on target, with less damage to the surrounding areas.’
Synthesis Ending: Catalyst Control Protocols (Military Strength: 600) Our scientists have decoded details from the Mars Archives data about the Catalyst's networking processes. This has lead to updates in the integration systems for when the two are connected, although the Catalyst's identity remains a mystery.’
All 3 Endings: Deciphered Crucible Documentation (Military Strength: 1000) ‘Our scientists have decoded further details from the Mars Archives data about the Crucible's purpose. They believe it is now possible to refine and improve the targeting systems.’
Achieving all 3 endings with multiple playthroughs on a single character would then allow you to push your EMS over 9,999 (Congrats on breaking the Scoreboard). Do this, and the Catalyst will instead remark about how you have completed and improved the Crucible beyond what it thought possible, and it will say that other synthetics will suffer ‘minor casualties’. Choosing the Destroy ending will then have several differences:
The Citadel will still be damaged, with explosions and lights going out, but not completely self-destruct. People are later shown clearing rubble and rescuing buried survivors in the Wards and on the Presidium.
The central rings of the Relays still explode, but the main body does not. The relays are later shown in the process of being repaired.
If the Geth survived Priority: Rannoch, they are shown being affected by the energy wave while fighting Reaper forces and knocked offline. Some (but not all) of them are then shown rebooting and climbing to their feet. If the Quarians also survived Priority: Rannoch, then they will be shown fighting alongside the Geth, and helping the surviving units to stand up.
When the Normandy is caught in the blast, we see shots of the controls and lights turning on and off inside (like when EDI moved into the mech after Priority: Palavan), EDI's mech body spasming in the co-pilot's chair, and the AI core wreathed in red lightning before going dark. When Joker and the other crewmate exit the crashed Normandy, they are supporting a limping and sparking EDI between them, her visor flickering on and off.
(This is, essentially, the high-EMS Destroy ending, only without the shoehorned-in negative consequences: you improve the Crucible's ability to target just the Reapers)
Good idea? Bad idea? Goes too far? Doesn't go far enough? Or, just fed up with people complaining about the ending?