I wrote this up earlier today. Word of warning, IT'S REALLY LONG.
I wouldn't change too much, really. Just tweak the Reapers' motives so it's more in-line with previous lore.
Oh, and Priority: Earth, if that's on the table.
P:E Opens with Shepard discussing preliminary tactics, the initial push to Earth, etc. Here, the player can draft up a basic strategy for the assault on Earth by assigning roles to their Fleet Assets. Will the Turian fleets lead the charge or will the humans? Or a mix of complementary fleets? Will the Reapers be engaged head-on so as to draw them away from the planetary invaders or will you focus on more precise and targeted strikes to take more of them out? Or split your fleets and do both? These decisions will affect how many troops make it to Earth and how the fleets fare later in the battle. The real work here would be the cinematic factor. Planning out the variables themselves isn't too difficult, but representing them, especially since there are several, several possible combinations, would be taxing.
Next, planetside tactics. Now it's a case of who goes where, and the level isn't even completely linear. I would likely split this mission into three segments, with unit assignments/reassignments at the end of each segment. Segment one focuses on taking down the Hades Cannon, which is in the middle of hotly contested territory. Here, Shepard has two options: he can either attack the cannon himself or create a diversion by destroying a harvesting facility while the main team attacks the cannon. For both scenarios, he has to assign a strike team war asset, and for the mission he doesn't choose, a squad member must lead the other team. If Shepard chooses his assets poorly, a squad member will die. For instance, sending the wrong team to the harvesting facility will result in the team either falling back in the face of heavy losses (which means the bulk of hostiles will now be focused on the cannon), resulting in a squad-member dying at the cannon, or the team can push on and a squadmate is killed in the facility. If the wrong team is sent to the cannon, the squadmate leading that team dies regardless, as the cannon must be destroyed. Send two wrong teams and you lose two squadmates, one at the facility and one at the cannon, or both at the cannon. If you only have one squadmate at the end of this segment, you will recieve a replacement in the form of Anderson for the next segment.
Once the Hades Cannon has been dealt with, the rest of the ground force is shipped in. Their strength depends on the actions of the fleet. If a strong fleet fights the Reapers head on, the assets will arrive relatively unharmed, though the fleet will take a 10% effectiveness hit. If a strong fleet engages more tactically, the arriving assets will take a 10% effectiveness hit. If you split the fleets, both fleet and infantry assets will take a 5% effectiveness hit. The amount of effectiveness lost increases the weaker your fleets are.
Now for the second stage of fleet maneuvers. Shepard can either order the fleets to press the assault and "clear the skies," or he can order the fleets to initiate a tactical retreat. The former would mean that ground units have an easier time of it at the cost of ships, while the latter gives the fleet a breather at the expense of soldiers.
I'm not exactly sure what I want to do with the FOB, so let's not touch that. Instead, we'll move onto the next tactical menu, the distribution of ground forces. It's time to rush the beam, and there are three ways to get there: a direct approach with heavy infantry and artillery (vanilla), a detour through less contested territory with strike teams and support, and a surgical push through occupied territory with spec-ops/commandos. Then, you choose which path to take, each with different objectives. For path one, it's similar to vanilla: take down the guardian Destroyer. Path two: establish a beachhead flanking the beam and prepare for the charge. Path three: eliminate high-priority targets and commit other acts of sabotage on the way to the beam. The difficulty of the three paths depends on what assets you assign. For example, accompanying Blue Suns on path two results in a more difficult run than accompanying marines, while a Spectre unit proves more effective than a Justiciar contingent on path three. Secondly, if you accompany assets with unique commanders, like Arlakh company, you will fight alongside said commanders, like Grunt. Ultimately, the effectiveness of your assigned assets determines how prepared you are for the beam rush. Assets not chosen remain at the FOB to hold the line. If they prove too weak, you will be flanked and may lose one of your assets.
Now for the final segment: the Crucible and Citadel. You've geared up for the beam rush and have amassed your armies around no-man's land. But suddenly, a group of Reaper's have broken off from the fleet and have begun heading for you! If you commanded the fleets to go on the offensive, the majority of this invasion force will be destroyed, provided your fleets have remained strong. If you commanded them to fall back, only some will be destroyed and the beam rush will be that much more desperate. Nevertheless, the charge has begun and you're running down one of the paths to the trench. Harbinger descends and opens fire, making a general mess of things. Depending on the strength of your assets, you will either make it to the beam with one, two or no squadmates. You might not even make it at all, going out in a blaze of glory. In that case, you'll be treated to a series of cutscenes depicting the defeat of what few combatants are left. The outcome of the charge is determined by how many Reapers make it to beam, as well as the strength of your infantry assets. Lone Reaper and medium assets means you're A-Okay, as does some Reapers and strong assets, and several Reapers and very strong assets.
You make it aboard the Citadel, and find yourself in a processing chamber. Another Human Reaper is under construction. You search for a way out of the chamber, ultimately finding yourself in a deconstructed presidium. A glance at the fleet battle shows that despite your best efforts, the fleets are ultimately losing and have called in the Crucible. What strength they have left determines its integrity. You head for the tower and the control panel within, possibly encountering pockets of resistance along the way (depending on your Citadel assets). Those pockets will join you in your push, and important characters may open up alternate passages along the way. When you finally make it to the tower with whatever force you've assembled, you encounter Anderson, who followed you up with his own battle-hardened team (Unless it's a worst-case-scenario playthrough in which Anderson is a squadmate). Once in the tower, you encounter TIM, standing over the control panel. As soon as you begin to approach him, he mutters something along the lines of "You're too late, Shepard," and ascends in a column of light (or on a hidden elevator). You call for evac for your squads and your resistance forces, and you and Anderson head on to confront TIM. Who makes it off safely is determined by the strength of your remaining Citadel Assets and Fleet Strength, with Fleet Strength being the most important for actually getting people off the station.
For the confrontation. I'd actually leave most of this alone, or would prefer to let someone else handle it.
Which brings us to the finale. Anderson has died and Shepard has ascended to the Catalyst's chamber. He is awoken by a pillar of light, or an orb of light. Whichever. The construct awakens him and marvels at the fact that such imperfect beings have managed to essentially defeat the Reapers. Now, instead of speaking about how the Reapers are his solution to the chaos (we'd have to tweak Levi a bit for this to work), it'd explain how the Reapers are the ultimate form of life and that, rather than exterminating races, the Reapers were ascending them to Reaper godhood. It turns out that the Reapers were intially born of an attempt to attain an effective synthetic immorality by merging the minds of an entire species into one ever-lasting form. The process failed, and the Reapers were born. Thus, the cycles. But now that they face defeat, it has become apparent that they are not the perfect beings they considered themselves, and so the Catalyst, their combined consciousness, can do nothing but allow Shepard to decide their fate via the Crucible.
And so, Shepard is presented with two options: he can assume control of the Reapers and do what he pleases with them, or he can purge them from the galaxy. Your Crucible and Fleet Assets will determine what the Crucible is ultimately capable of, as will your collector base decision. Interestingly enough, the base decision has a somewhat opposite effect on the Crucible choices. Saving the base allows the Crucible to precisely target Reaper AI, sparing the Geth and EDI, but now it doesn't have the sheer power to utterly rewrite their AI, instead allowing Shep only to reprogram them. Conversely, destroying the base gives Shep the juice to overwrite the Catalyst and take full control over the Reapers, but the overcharged Crucible completely wipes anything running on Reaper AI. Regardless, the relays are destroyed in the beam dispersion. A damaged crucible would become exceedingly less effective, either stunning the Reapers only temporarily, or causing ever-greater collateral damage. It might not work at all.
And, then cue epilogue. Not sure how I'd handle this either.