I would've ended it the way the game was advertised: take back Earth.
The team from Mass Effect 2 is never split apart. The Priority: Earth mission lasts longer. Throughout the mission, Harbinger assumes direct control here and there to make Shepard's life all the more challenging.
On Earth, you play through several missions similar to Mass Effect 2 where you assign your war assets to different missions, then play through the results. For example, you could put Zaeed in charge of the Blue Suns to spearhead an attack, while Garrus leads a group of turian commandos, and so on. These dramatically change how the battles look and play out. You get to control a Mako or a Hammerhead during one or more battles, too. The battles are bloody but Reaper forces are pushed back to London.
Meanwhile, friendly forces on the Citadel -- possibly led by Shepard's love interest and other team members ;-) -- have been desperately holding off Reaper troops. The Reapers want to put their Catalyst -- the Illusive Man -- into the control room so that he'll use the Crucible to send a massive EMP pulse across the galaxy. This will leave organics helpless without their technology and will disable or disorient geth so they can be reprogrammed. If our Catalyst -- Shepard -- gets there first, he or she can use the Crucible to control or destroy the Reapers.
Forget about the beam run. Friendly forces on the Citadel manage to open the Citadel's arms just enough for the Normandy to fly in and drop off our heroes. Similar to Mass Effect 2, you have to choose different team members to lead different parts of the final mission.
The battle with the Illusive Man is suitably apocalyptic
. Meanwhile, outside, Harbinger is fighting his way through the fleet trying to get to the Citadel. When Shepard kills the Illusive Man, Harbinger loses control of the Illusive Man. As he dies, he says, "Thank you, Shepard," screams, and sends out a blast of power that disorients Harbinger and allows the fleet to destroy it.
Shepard faces the control panel. Using "Prothean-vision", Shepard realizes that the Crucible is a junction box of the power of the mass relays. Shepard can use it however he or she chooses. Shepard's love interest raises the question of whether destroying the Reapers means that cycles of destruction and extinction will begin again. Shepard's response options are basically:
Paragon: "We have to have faith. If we work together, and we deserve to, we'll survive."
Renegade: "Never. We'll shape the future."
I'm too lazy to work out the three options on the right side of the conversation wheel
.
Shepard is hit with a blast of energy and lifted into the air. The Crucible fires. Geth are not destroyed by the Crucible effect. When it's over, Shepard drops to the ground. Renegade Shepard controls the Reapers and is immortal. Paragon Shepard experiences visions during the Crucible effect. While not immortal, Shepard has gained some of the aeons of knowledge of the Reapers, which will help the races to rebuild.
The last mission, Priority: Citadel, unlocks. This plays out the beginning of everyone's life after the game, and is mostly a love note to the Normandy team.