I'd change ME3 this way.
Tone down Cerberus's dominance and make TIM not-indoctrinated and occasionally helpful to Shepard (to his own motivations: the survival of mankind, the advancement of humanity through non-harmful reaper-tech implants or upgrades, via reverse engineering perhaps)
Define what goes into the Crucible's design early on. "Mass Effect similar energy" and learning that it fires by using the Citadel as a starmap and power-source to target and disrupt Mass Relays and all Reaper-tech.
The Crucible development would lead into a finale that included a dilemma on whether to fire the Crucible or not or focus on accumulated military strength.
In this version Sanctuary doesn't produce an army, just reverse-engineers reaper tech.
- If you decide to stand against using the crucible, you must convince Hackett why it must be that way. If you unsuccesfully argue, Hackett becomes semi-antagonist. Conventional victory (if EMS is high) is achieved but Shepard is deemed traitor and loses his rank. If you succesfully argue, Hackett aknowledges Shepard's decision and and all's well if your EMS is high and conventional victory is possible.
- If you decide to use the Crucible, TIM will intervene. Through his reverse engineering and Sancturary's research he is convinced it can be applied to the Crucible in order to extract dark-energy from the Reapers' technology, as well as ending them. He wants Dark Energy extracted, so it can be used to advance humanity's role in galactic technology, and for "whatever may come up in the future". If you succesfully talk him out of it you fire the Crucible which halts the Reaper-cycle, cleansing the galaxy of their tyranny for good. If you aren't succesful or simply agree with his proposal, he injects a piece of technology (placeholder) into the Crucible's firing chamber , the Crucible fires and disrupts all Mass Relays and Reaper tech. A post-credits scene for this outcome will show a disabled reaper twitching its tentacle, as if to imply they might reawaken some day. In order to extract Dark Energy TIM needed the Relays and Reapers merely in a slumbering state.
Something like this. I basically wanted it to be simpler but have some tension between the factions you've worked for in ME1 and ME2 respectively, and in a way that also meant it would feel like both games were properly represented in ME3's story-arc. The Dark Energy plotline wouldn't really be an explicit part of the plot, but there's an aspect of "speculations from everyone" to this idea of the plot that would've probably left us pondering "why DID TIM want Dark Energy extracted`, and for what?"
Alternatively, rather than using the crucible to disrupt the reapers and shut them down, it would simply disrupt them and the military force you've gathered would have a slow, methodical but guaranteed victory.
I also considered altering it so instead of Dark Energy, TIM would just somehow be able to alter the effect of the Crucible so he could extract the Reaper tech (as it wasn't completely out of function after being disabled) to simply improve humanity's edge in technology and put them on the seat in the galactic tech-scene in a near future, or he would sell his technology for moneyz and live the rest of his days on Illium with Asari strippers and fast hovercars.