Honestly, I think there would have to be a very extensive rewrite for the games in general. Starting with the first one, I think indoctrination should be handled consistently. I don't mind the party not knowing how it works, but the writing itself isn't consistent enough. They strung a lot of the story together in the second and third game in the most half-assed way, like the dreams about burnt forests as a marker of indoctrination which is bs, but some of that stuff was great (like the Cerberus team who try to get the reaper IFF and, once indoctrination sets in, can't tell their memories apart anymore).

For the second one the most important change would be that Shepard doesn't die and has to be brought back. It makes no sense to handwave that much of human biology to justify that you can restore a deep frozen human brain to its original state. Having the Normandy be destroyed in the beginning is impactful enough, and having a lot of the crew survive but shipless would have been acceptable too. It would make a lot of sense to me if the beginning of the second game was just the crew stranded, getting saved and then there's a two year jump to the present with the abducted colonies. Maybe Shepard was injured and had to retrain to get back to form (explains the character creator popping up), only to be sent out to one of the colonies where you could meet both Tali and maybe also Miranda and Jacob. Re-introducing Shepard from an "I am an Alliance soldier" perspective makes the most sense, and I'm pretty sure its possible to not kill Miranda and Jacob on the first meeting. Shepard might also be able to join the Virmire surivor's mission to find out if Cerberus is behind the abductions.

That amount of changes alone would rewrite the majority of the second game, and that would lead to a shitton of changes in the third one. If we were to keep the games as they were up until the ending, I think I would've appreciated if the ending really turned out to be that Shepard is indoctrinated. I honestly thought indoctrination was a fun plot point that makes everything a lot more risky and once it's too late, there is nothing you can do about it. I would even appreciate if Shepard would realize they're indoctrinated as they're talking to the Illusive Man, and after taking him out, also taking themselves out in a similar manner to Saren. There's a bunch of supposedly very smart people working on the crucible (as bad as it is as a story point), somebody would figure out how to use the thing, they've been winging it up until then anyway.

That's just off the top of my head, and I think I would still be salty that the original games went the way they did.