I'd expand out the Sanctuary-onwards bit to mirror the preceding two acts. End the Cerberus story there with either destroying them entirely, allowing the Illusive Man to continue, or installing Miranda (if alive) as the new head of Cerberus. With a secondary choice on whether to keep indoctrinating human as soldier or not.
Have a few different routes and options for the assault on earth that requires you to make choices on utilising the war assets at some point - if you have Krogan, a ground assault makes more sense, Salarians, something more sneaky. Same for Geth /Quarian or if you have Cerberus troops or not. Stupid choices mean people die, but in cases where you have both you can get some awesome saves in.
All this (+ MP score if you must) factors into if 0, 1 or 2 of your squad make the beam with you. Also if Anderson makes it.
We lose the explanation of the Reapers (or go dark energy, or anything that makes more sense) - the Crucible is there on the basis that it was made as a way to end the cycle if the races were advanced enough that they could handle whatever 'problem' the Reapers are fixing on their own. The star-child is still there to explain this, but takes the form of the squadmate that died on Virmire rather than a kid (I mean come on Bioware, how did you not figure that out?).
The options are a result of conversations between Anderson, your possible squadmates and TIM/Miranda (who somehow got there - needs one plothole to be authentically Bioware).
Control: If you destroyed Cerberus entirely, Control is not an option. It's made clear that control will see whoever takes control of The Reapers living forever in a constant mental fight to stay on top - a huge sacrifice for Shep to make. If you installed Miranda as head of Cerberus, and she's loyal and still alive, she'll offer to do it ("this is what I was made for Shepard").
Destroy: You need either Anderson or an 'aggressive' squad mate with you to get offered this (Ash, Vega, Javik and Tali if you killed the Geth) - it still destroys all AI (but not people with implants like Shep), and also blows up the Citadel. With a high enough readiness, Joker will be able to navigate a path through to the Citadel and send a shuttle for you, in which case Anderson, Javik or Ash will be able to opt to stay behind and hit the button while you escape. You might not want to mention to Joker what will happen to EDI.
Synthesis: this gets offered by the 'ghost' of the squadmate that died on Virmire, only if you made peace between either the Geth/Quarian or Krogan/Turian. It's a re-sequencing of DNA that unites all species, a forced evolutionary step. It's explained better, and the downsides are drawn out too. I think it needs a sacrifice component too so it's not the obvious 'good' choice - maybe it needs to harvest DNA of three species or something. Or maybe it needs dropping for an entirely different option but I'm trying not to re-write the whole thing.
Nothing: if you don't meet any of the criteria, the crucible doesn't work and the galaxy gets blow up. Likewise you can walk away and not make a choice to similar effect.
Regardless of the ending you choose, depending on their disposition towards you various squad members may forcibly want to stop you making certain choices, forcing you to kill them. Feasibly, if you choose to walk away, they might settle it between themselves instead.
The Mass Relays are slowly deactivated rather than blown-up - they'll remain functional for around a year as they degrade.