I will bite.
ME1: I wouldn't really change much. Maybe the combat but that is it. The atmosphere, the tone, and the story were pretty good. If I could change anything about the story, I would include something that states (either via Rana or via datapad) that the prothean obelisk found on Virmire was found after Eden Prime. Also, I would make it so shepard could only level to 30.
ME2: Ok...now we are going to have some fun.
Mechanically I think it is fine. Good mix of powers. Good facial scarring via paragon/Renegade. Overall, the mechanics and the pew pew are quite good. Increase the level cap to 60
Now...to the story:
Shep wouldn't die in the intro. Most likely I would have the normandy attacked - as that was actually a very sound introduction back into the game. Shep could then have the choice to save crew members or escape. If the former is taken many more crew members would survive and shep would escape - but harmed. If the latter is taken then shep escapes unharmed. By harmed I would probably have him/her lose a limb and some level points.
Now, I would still have us fightng mercs...Yes yes I know it is silly but the reason I would have for it is that post battle of the Citadel the merc groups have gained more footing due to the now rebuilding council fleet (which has retreated to only protect core worlds - leaving many colonies undefended). This allows the collectors some leverage when abducting human colonies. Depending on how much you fight the mercs in ME2 it will reflect on how scattered or strong they are in ME3. EG if you just annihilate the blue suns, eclipse, and blood pack in ME2, come ME3 they are barely a shadow.
In collector missions I would probably have some missions where shepard is given the choice to either save colonists or salvage collector technology. Oh, and no Harbinger Taunts. He would either comment on Sheps squadmates and issue orders. That is it.
I would keep the recruitment missions and the loyalty missions, as I would focus ME2's core story mechanic on the squad.
I would have a side story that deals with the shadow broker and would culminate in the defeat of the broker and the finding of the crucible plans.
The finale would be the sucide mission - no change in gameplay or how it plays out. Rather than a baby terminator though i would probably just have what looks like a tentacled mass with a few eyes. Something that looks like a developing fetus that is all reaper tech. Give the audience something to really process.
I would set Arrival AFTER the suicide mission (you will see why in my ME3 redo)
ME3: Ah, what could have been. Increase Level cap to 90/100.
The intro would be the trial. No ifs, ands or buts.
- I suppose we could have a subplot where the batarians try to kill shep, but I am going with the idea that the batarian homeworld is kaput at this point.
The trial would be interrupted via a reaper attack.
Things would play out rather normally, but rather than a quick run and gun mission I would have shep given the choice to rescue civilians or military. No matter what, the kid will still dye. This will help/hurt sheps fighting forces in the end-game.
Mars should play out the way it did - no real issue there
Overall, I would have shep explore and aid/destroy worlds he/she goes to. EG if you are on Feros and you saved the colony when you go to help them you are aided by the enhanced colonists or you are looking at a slaughter (this again helps/hurts your war resources)
In addition I would break the War Asset calculator into:
Military
Crucible
Shep would be on a mission across the galaxy to both rally military forces and gather components for the crucible. Your MP war readiness only would affect the Military portion of the War Assets.
Tuchanka arc is the same. I liked it
The citadel coup wouldn't happen - that was just stupid. Instead, I would have a Battle of Palaven arc. You use your new Krogan/Salarian forces to help evac Turian Military or Civilians. Garrus is mandatory and can die here. Evacing civilians saves his family. Evacing military kills them. Depending on his loyalty to you in ME2 he will either kill himself (disloyal) or just be depressed (loyal). By now we find that due to the events of Arrival and ME1 the journey to the galaxy has made the reapers very vulnerable.
The side story would be the Cerberus war which obviously ends at Chronos but largely ends in the battle of omega. Omega will have 3 stages:
1- assault
2- capture
3-Defend/Sacrifice
in act 3 of Omega, Harbinger would come in with a reaper army to take Omega and the player is given the choice to sacrifice Omega or Defend it. Defend would have a heavy Military asset cost.
Then comes the Leviathan arc. Mostly the same I guess.
Then comes Rannoch. Mostly the same. Though in the end you can either Keep the Geth as they are or upload reaper code. Either way you are forced into a fight with the quarians v geth. One or both can survive based on prior choices
By now the Crucible should have nearly everything needed minus the final component - the catalyst (lol)
Then comes Thessia. I would make the main mission largely what we got but add in two minor missions that help/hurt the main mission. For starters, yes Kai Lame would show up...can't really avoid that. But he would be a bit more...how we say...threatening. I always envisioned Leng as a wannabe shepard. He would have heavy augments and in the finale of Thessia you can fight leng as the temple crashes down. Liara can die/ not die based on choice
Then we get a signal to go to Horizon. The mission plays out the way it did, just with more body horror. you will see half-turned husks, lots of corpses, read about cannibalism and mass histeria. Like real desperation at the place before it was raided by the alliance (not the reapers). Here we get an end to the Miranda arc.
Finally come Chronos. Here we resolve the Cerberus arch and kill Leng and TIM (who dies by proxy of the fighting or by choice...not sure yet)
Due to reaper implants in the cerberus troops we learn that TIM lost all control over his minions and was executed by leng very early in the war (the holograms of him were just holograms) TIMs last effort was to aid shepard (he sent the signal to go to Horizon) and crew in retrieving the catalyst. The catalyst is revealed to be the citadel and the object which can focus the crucible energy.
We then realize that, during the assault on Chronos, the reapers have taken the citadel (Cerberus was just used as a diversion to make the citadel vulnerable).
We launch an attack on Earth with everything we have left.
Now, the fun part.
Priority Earth would have about 4 routes to get to the beam. These routes depend on EMS and Military Strength. In addition to Reaper strength (remember all those save the civilians or military side missions and such. Ya this would come into play here). In this finale you would have multiple stages where you are given the sadistic choice to either sacrifice a squadmate or save military assets. Near the end, coats would be dead and it would be down to shepard to command the forces at the beam (like a commander should). Anderson set the plan, Shepard executes it.
We take down the destroyer as normal, but finally FINALLY we get a showdown with Harbinger (or a Sovereign class reaper if this is a ME3 only playthrough). The battle can go one of three ways:
1- Harbinger kills everything = you lose
2- Harbinger Kills almost everything except shep and is wounded
3- Harbinger kills a lot but is wounded and must retreat (or calls in reinforcements...not sure)
The finale would be a mirror of the battle for the citadel in ME1. Except now you are fighting alone and with C-Sec or Fighting with your two sqaudmates and with C-Sec.
Harbinger would then make it to the citadel tower (once it is opened) and shep would then have to call in fleet support to take it down (as it has assumed control over the citadel). The fleets would be successful in killing Harbinger and - in the resulting explosion - shep is critically wounded and the squadmates are knocked out.
The crucible docks and shepard is carried (by way of the keepers) to a secret area. The catalyst.
The catalyst tells shepard that the reapers are its creations and were created to both solve the problem of synthetic life killing organic life. However, upon completion of the reapers they attained their own consciousness and -seeing themselves as perfection - sought to remake all life in their image as perfection.
Shep is then given the choice:
1- Destroy the Reapers
2 - Control the Reapers
Destroy would have high, med, and low
Control would have High (control permanently sustained) or Low (control is attained, but for how long?)
Shep can possibly live in the Destroy ending.
The crucible fires and the Cycle ends.
Enter our slide shows (with narration) and we get our resolution. Oh, an no jungle planet. No one jumped out of the system. The relays are either non-functional or damaged and non functional post choice.
And that is about it. That is honestly what I would change...but I am a simple man and I am sure I forgot some things.