I know that BioWare has decided to NOT make a new ending and just try to "clarify" the ending we got, but I just want to share my own ideas for a possible new ending, so here it goes:
Your squad-mates will end up dead regardless if your EMS is high or low. The EMS system shouldn't work that way, it would make sense if your square-mates die from Harbinger's beam because a lot of the squad-mates are willing to sacrifice themselves to defeat the Reapers. If possible, there would be a cutscene where Shepard's love interest would survive long enough to tell Shepard how much he/she loves him/her before dying. That would be the most emotional, heartbreaking moment in the entire series.
Following a confrontation with the Illusive Man, Shepard is lured into a final battle against Harbinger. I don't know how Shepard would fight Harbinger despite his/her injuries, but there should be a way for him/her to defeat the Reaper without having to run around and dodge it's attacks. After defeating Harbinger, Shepard has the opportunity to activate the Crucible. However, there are two ways to activate the Crucible, and one would ultimately lead to his/her death.
If your War Assets are high enough a you made a lot good decisions throughout the past three games, neither of the two choices will lead to dire consequences, like wiping out an entire fleet or ridding the galaxy of synthetics just to destroy the reapers once and for all. You can decide if Shepard will live or die in the end, because no matter which option you choose, you still save the Galaxy. :)
And there you have it! My own idea on a new ending. Sorry I haven't gotten into greater details, I'll probably make a part 2. I know that some people would disagree that this is what the ending of Mass Effect 3 would be like, but it's just my imagination. You can share own ideas on the comments below.