I agree with this so much. I think the whole concept of killing and resurrecting Shepard, and having him work with one of the tertiary villains in ME1 is a conceptual misstep. There are lots of stories that could have centered on the building a team and then going on a suicide mission together once your invested in all the characters.ME2, despite being a series high point, completely derailed the story
I actually think something about cleaning out the surviving Geth from ME1 ending, culminating in a mission on Rannoch from ME3 could have been a really nice middle step to the Reaper invasion starting ME3. But I'm just some random dude on the internet, so it would probably be terrible when blown up to full game narrative scale.