So here's what I would have done, since you asked me.
The true enemy is not the Reapers; it is in fact a great Alien Empire, and this empire is composed of and exists within the Dark Matter of the universe.
A plot along these lines would be easy to believe, given the allusions to Dark Energy in ME2. Also, Mass Effect would get hard sci-fi credit for working in another real scientific concept.
In this alternate reality where the writers were given time to make something good, the Reaper plot to protect us from ourselves actually makes sense. In this Mass Effect, the Dark Matter civilization is massively xenophobic, and has conquered everything they have ever met except the Light Matter universe (which Neil deGrasse Tyson would tell you interacts with them only through gravity). This way, the Reapers have a reason to exist, and we can re-write the critical plot of ME3.
The Reapers are the loyal servant AIs of the first civilization of Light Matter entities, who ascended in technology far enough to interact with Dark Matter. They opened the gate the Dark Matter beings could not. The result was a near-total destruction of all intelligent Light Matter life at the time, a terrible reprisal of the fearful and fearsome Dark Matter beings. The Reapers managed to end the effect their masters started, but not in time to save them.
A pale shadow of their masters' once great civilization, terrified and terrible the Reapers wait in deep space for indications of any civilization advancing far enough to interact with Dark Matter or energy again. They remain ever vigilant, destroying colonies or entire races that are on the verge of a breakthrough to expose the galaxy again to the Dark Energy beings. Occasionally, a civilization spanning the entire galaxy, such as the current Citadel Council, reaches a point where it is inevitable for multiple races, governments, colonies, or individual research groups to make the breakthrough many times or in many places. When this occurs, the Reapers reach a decision to bomb the entire galaxy back to the stone age. Dependent on them themselves, the Reapers leave the mass effect relays and the citadel intact, but driven mad with loss and without the guidance of their original masters, they are unable to change or seek a way to aid the new races.
This sets aside the idea of a regular 50,000 clock for the Reapers.
Why change all this though? Most people don't seem to really care that much about the sci fi making sense in games, or movies or even books. Because then the following makes sense:
Did Star Wars end with Luke meeting the Emperor and choosing one of three buttons? No. He fought his way on board and faced the evil while his friends fought the good fight outside, and then he escaped while it blew up.
So what to do with Mass Effect is simple.
Shepard's final battle is now to get on board a Reaper and reach its brain. Bear with me.
With Shepard's convincing, the Illusive Man presents the knowledge he has gathered, from Reaper artifacts and the disable Reaper from ME2, to a joint project to stop the Reapers. A project composed of any combination of Alliance, Cerberus, and Council scientists, as well as Legion-aligned Geth and EDI. This project has the goal of creating a program and appropriate interface capable of being connected to a Reaper 'brain' directly, using the Reaper to broadcast the program to other Reapers, and in some way alter the Reapers it is spread to. Of course, how exactly to 'alter' the Reapers can be left to Shepard. This leaves room for a revised 3 endings, and many more.
The Crucible, previously in the role of the program, can thus either be a weapon capable of disabling a Reaper by firing upon it, or capable of briefly disabling all Reapers (and other AI's?) within a star system at once, or it can just be a death-star-cannon that shoots hole in them, or anything you want really. Use it as a plot device for aiding the allied forces fighting the Reapers, giving Shepard the cover and time he needs to get on board a Reaper and approach the center of whatever it has for a nervous system.
And so we get to the real point: now Mass Effect ends with a battle. A huge space battle, of course, but Shepard actually does something! Not on the surface of a planet, in a human city, where any halfway intelligent Reapers would never be because they simply bombed it from orbit. Instead, Shepard's allies dramatically fight the Reapers in space, and he enters a critically damaged, or temporarily disabled Reaper with his crack team of characters you've spent the game with. First underneath torn hull plating exposed to space, then through bays holding husk shock troops, and finally escaping into the belly of the beast, Shepard fights his way to the center of its living AI and injects his chosen variant of the Plot Device.
But the game will not end with pressing a button. As the Reaper he has assaulted transmits its ingenious virus to all the others, it begins to crumble. Burning in space, pummeled by allied fire, beaten into submission by the superweapon that disabled it, and wracked by internal damage committed by Shepard's team tearing their way into its guts, it's mass effect core begins to fail as its secondary systems fail and overload or overheat.
And so it is time for the final sequence. A short fight takes Shepard's team to a previously-established vehicle. They pile in, possibly taking more than one, possibly commandeering them with EDI's hacking help etc, and pilot them under the player's control dramatically through the cracking structure of the Reaper, along its hull, and within range of a Normandy pickup. If you want to know how to do it right, play the end of the first Halo probably and go from there.
The Reaper explodes in stages, and then warps in on itself as its core fails, providing a foreground to a battle filled with Reapers in various stages of shutdown.
There's a ceremony, Anderson gives a speech appropriate to the choices your Shepard has made, your romance interest is there at your side, your loyal friends looking on. You get a medal or several. There are a series of short cinematics for the endings your crew members got, and where they departed to. Some of the endings imply teammates working on ways to approach the Dark Matter universe problem. Finally, Shepard stands on the bridge of the empty Normandy, dimly lit in a spaceport orbiting Earth and undergoing repairs. He runs his fingers along the surface next to the galaxy map projection. It flickers to life. He raises his eyes, gazes piercingly into the star chart, and then lifts his gave again past it to the stars visible through the helm window. The map's light glimmers in his eyes, and his somber expression rises to a smile of challenge.
The screen flicks black as heroic music crescendoes.
Don't forget some concept art.
After this, let the player create a save, and then load an EndGame+ setting. I include this for EA, so there's a way for players for play the DLC they'll want to release with their Shepard in all his glory.
Of course this leaves obvious room for a future Mass Effect, possibly with a descendant of your Shepard, to deal with the Dark Matter beings in some way. Alternatively, they could be characterized as howling demons, kept at bay by the closed portal to hell, implying no need for a follow-up.