No different than if Bioware had never made an ME4. Stories end. You need to come to terms with that. Again, no amount of thought and effort will allow an overcooked burger to turn into a masterpiece.
And regarding canonized choices: again, big talk on that point. Sure, it might be preferable for you. But I for one wouldn't be touching that version of ME:A. The question though isn't what you or me want. The question is what sustains Bioware's future? Mass Effect 3 caused one of the more dramatic ending crises in recent history. It was meant as the epic conclusion to the Shepard trilogy and (for many) it failed. Writing a competent story is tough enough on its own. Now write one that has to stand entirely on its own while taking into account an entire trilogy's worth of choices and a massive controversy on top of it. Now add on a canonized choice which will immediately turn off certain players. And tack on that ME4 won't fix most of the ending issues (Catalyst logic, Synthesis Space Magic, Shepard dying) to any satisfactory extent.
What ideas do you actually have to offer here that go beyond "just put some thought and effort into it"? Because that's pretty weak in the context of ME3. The point of Retake was to fix Mass Effect 3. This does not fix Mass Effect 3 to any satisfaction. It throws a band aid on 3 years too late.
The trilogy ending wouldn't be an over cooked burger as it's not broken, it would be a burger with banana's, maple syrup pancakes and a patty of soy. You don't have to go back to fix anything, just adjust how you move forward after eating it. So in this case, in order for the galaxy to continue you need to choose the ending choices that make the most sense for continuing on with the MW as canon. This is what Bioware / Mass Effects future needs to be.
Turning off some players will happen no matter what choice they choose, specific canonized ending to going to another galaxy. But out of it all what is best for continuing the IP? If they are going to continue with the universe, then the decisions of the MW had to be made, and it would have to be a canonized choices to determine how it fits with the stories in other galaxies, because eventually there will be contact.
So for all the choices that survive the Reaping, they didn't just mysteriously forget they sent off an Ark to Andromeda. You don't think they would then try to reach out to that Ark to say we are ok, but more so to set up a support structure of communication? We are willing to wait months or years to communicate with our own probes of our system that are far out, and sure it wouldn't be a problem here. Because now we have just won the Reaper war and also sent out an Ark to another galaxy which is now a great extension to our empire.
1) Which isn't really relevant. If Bioware had decided to never make another ME game, the choices don't stop being meaningless. Jade Empire has never had a sequel. Are those choices meaningless? They occurred and they presumably effect the galaxy at large.
2) Well, beyond the Genophage. Oh and the Geth/Quarian War. Not to mention the Rachni (at least in theory). And the endings themselves, which would have to be canonized, since Destroy, Control, and Synthesis all lead to rapidly different galaxies. Which goes against the whole "fix the endings" scheme you've imagined. You accuse Bioware of burying their heads in the sand. This honestly sounds more like you want them to cater to your whims, all consequences be damned. Once more: How does any of this fix Synthesis, Catalyst logic, Shepard's death, so and so forth.
If BW decided to never make another game then your decisions would stand for how that IP was left off. The issue arises when they decided to continue the universe and decided to ignore what has already happened, as they occurred and they would effect both galaxies at large. Because if the MW survives the Reapers then I would believe that they would not abandon their people of the Ark, with reasons why depending on ending choices.
So if they continued Jade Empire, I would fully expect them to take into account the previous game otherwise what's the point of using that IP? They might as well just make stand alone games that are all variations of each other but not the same world. Just like the next ME game, it makes far more sense that if they want to keep it in the same universe then address the ending of the trilogy and move forward, or just create it as a remake, retake variation with no connection at all new game, aka completely different game.
Otherwise they have what they've got right now, which is a game that has left the vast majority of its fanbase with confidence that the story (the beggining) will make no sense. I don't think I've seen a single post here or anywhere from anyone that thinks this. A handful of writers most likely will not come up with something that their large fanbase wracking their brains hasn't.