I'd want Destroy to have two versions. One final choice for Shepard if he/she decides to shoot the tube:
1) Focused blast. Destroys all synthetic life, but tech like the relays is okay.
2) Dispersed blast. Destroys Reapers, other synthetic life survives. But much of the technology galactic civilization depends on is damaged. The "galactic dark age" that was mentioned way back when.
Well, Destroy doing what it does in the current endings I don't mind, since it's apart of the theme they're trying to tell at the end of the game. However, I'd want a 4th crucible option, which we never got. If you read my feedback DLC idea here, you'd know I'd want some mission before the end of the game, that would focused on Harb, and obtaining some kind of new data. And somehow this data would create a 4th crucible option that allowed you to defeat the Reapers without picking the other 3 options.
Well, I gave it some more thought. From a game design perspective, if you're keeping the current endings, but adding a new one, you need to add balance so there's no specific good ending still. And the best way to do that is to allow Shepard to defeat the Reapers, but at a new price.
So my new idea would be to have a story that explores someone studying the energy in the crucible. They discover how the energy could be used to destroy, control, or create synthesis, and give us a proper setup for it. However, the problem is, you need the mother of huge computers in order to tell the energy to do specific things (AKA the Catalyst), a way of firing it, and possibly mixing some elements to create the needed blast (like with Synthesis). But assuming all options can't be used, and the Catalyst is never found, the scientist creates a 4th solution where the energy is used as an EMP instead if Shepard throws a certain device inside the beam. The EMP would affect only Reaper tech, and briefly disable them for a few minutes, allowing the fleets to take a few out; enough to even the numbers before the Reapers came back online. Once they're back, if you have enough assets, it's clear the fleets can defeat the Reapers, even if doing so would deplete the fleets to 10% by the time every Reaper is killed. Shepard then gives the Catalyst three choices: Die, Surrender, or Retreat. Because if it doesn't back down, there will be no Reapers left to complete it's purpose, even if a lot of people will die in the process.
The Catatyst, pissed off, decides to go all out, and attack every leader as a last ditch effort. Wrex is killed. The Turian Primarch is killed. Hackett is killed. The Quarian leaders are killed. The Geth take heavy losses trying to save the remaining Quarian fleets. While this is happening, the Catalyst is trying to killed Shepard, and Shepard tries to get away. Even fights indoctrination. You then play your ME1 and ME2 squadmates as they land on the Citadel, and fight their way to Shepard. They then find out where the Catalyst is on the Citadel, and kill it. And mission to get to it, similar to the Suicide Mission, would get squadmates killed. You'd then destroy the Catalyst's Blue Box, but before it dies, it tells the Reapers to retreat back to Dark Space.
So the game would end with Shepard officially alive, but with a lot more squadmates dead, and a lot of things unresolved and undone. Instead of destroying the Reapers, they're still a threat that one day might come back. Instead of solving the Krogan problem peacefully with Wrex, the Krogan are now leaderless, the survivors are still violent, and with less numbers if you didn't cure them. The surviving Quarians, now leaderless, still mistrust the geth, and refuse to share the same planet with them, possibly causing another war. And if you did believe in the Catalyst's issue, that problem remains unsolved without a solution. So pretty much you undid what Paragon Shepard spent 3 games trying to achieve (Make peace. Bright futures for everyone. Reapers dead. And everyone alive). And the only way to get everyone alive and get the brightest future for everyone is to pick the 3 original endings. That would create the balance, where there is no "best" ending for everyone. It comes down to what's best for you.
But even though things are bleak, there's still hope. That the new problems of today might be solved later. And it's now up to the galaxy to try again, and decide for itself on what happens next, instead of being run by the will of one AI, or the choice of one man.