I hated the ME3 ending, for many reasons, but mostly since it fell so short of my expectations based on ME2. But not because it wasn't a rosy happy ending. The problem was that it hinged on a plot device that no one, in game or out, seemed to understand. Following is my attempt to build up an ending structure to satisfy different tastes, with sufficient plot resolution, but room for mixed results.
[spoilers]
I think successful plot devices fall in to two broad categories - complex devices that are fully explained, or simple devices that have a self-evident purpose. In ME1, there was the beacon, the cipher, and the conduit, all of which were reasonably simple. The beacon was an alien transmitter of visions - the cipher was necessary to make the beacon visions more readable. Given the background context of mass relays, the conduit was also easy to understand in the end. They even explained that it was one-way only. ME2 had the nefarious human kidnappings, that were eventually explained - they were building a human reaper.
ME3 - the Crucible was intended to stop the Reapers, somehow. Over the entire course of the game, no one ever manages to explain how it's going to work, or even how it's not going to work. It was a complex, alien device, but with the plans and all the experts you recruited, you could make some educated guesses. Does it include large quantities of explosive material - no, then it's probably not a giant bomb. A giant space-laser? A transmitter of some kind? Also desperately sad that no one on the engineering team noticed its five docking arms, of comparable size and shape to the OTHER giant space device, and put two and two together.
So - to change the ending, I would start by having a clear idea of what the Crucible actually does. Slightly arbitrary explanation: the Crucible mimics the technology used to communicate orders to the first Reapers (possibly based on the mysterious dark energy subplot that fizzled out). In theory it will allow new programming to be imposed on the entire Reaper fleet- however, it takes a tremendous amount of energy to power it, so the new command will have to be short and sweet. Borrowing from the original - the Citadel will act as a giant battery for it. This is the plan, though the actual command is undecided as yet. The player could be offered the choice of who to let in on this plan, cementing or damaging relations with the various factions.
Now for plot conflict, again an arbitrary mixture of ideas - TIM is also making a play for the Citadel, to use it to transmit his choice of instructions. Shepard and Co must fight TIM for control of the Citadel on the ground, and just to fudge things up even more, the plan has leaked to the Reapers, who are ALSO vying for the Citadel. Unfortunately, since it's their tech, the Reapers achieve control, and move the Citadel, passengers and all, to Earth. The fleet and Normandy follow, in a desperate attempt to punch through and use the crucible.
A CONTINGENCY PLAN is now formed - something lacking in the original. Since the Reapers are massed in the Sol system, failing all else, the fleet can destroy the Sol relay, Earth, and hopefully, the majority of the Reapers. This is what happens if your Effective Military Strength is poor. If you have a decent EMS, you can go ahead and try and connect the Citadel and Crucible - casualties depend on your resources. Possibly the geth and/or EDI, if they're friendly/still alive, can help you retake control of the Citadel. Ultimately you can choose what the Crucible relays to the Reapers, depending on how long you can hold the Citadel for:
* Low EMS - the Reapers selfdestruct on your command, doing substantial damage to Earth
* Medium EMS - most of the Reapers shut down benignly, although some selfdestruct (moral options include shutting them down permanently, deliberately burning out their circuits, etc; or shutting them down temporarily, ready to be rebooted at (and hopefully under) your command)
* High EMS - you successfully shut down the Reapers, with minimal damage, and have plenty of time to choose what to do with them. Besides the destruction meted out to reach this point, and all.
* Failure - the fleets and/or the Citadel can be destroyed by the Reapers before you get to implement your choices, or during your transmission, if you pick something more complicated than immediate selfdestruct.
The player can easily manipulate their EMS, to experience their preferred degree of success or failure, like in ME2. If you do every quest, and prepare like crazy, you can get a pretty assured win (though in ME2, I would still be on tenterhooks until the cutscene of joyous survival played). You can also fail on purpose, just to see what will happen.
On a side note, I would abandon the starchild - and the later stargazer and cute kiddie - as completely unnecessary fluff. My emotional investment lay with the characters developed over the trilogy, and the generic next generation evokes no sympathy whatsoever. It also undercuts the effectiveness of the much earlier child, killed off in the opening scenes - THAT was poignant, so stop there and don't milk it.