Good question, because I've wondered the same thing... I mean there have to be some good ideas, right? I see a couple here. First, I’m not offended if others have different ideas or preferences- so don't be if I'm on a different page, no offense is intended.
I want to add some comments that might allow thoughtful consideration. However, it's clear many people are simply interested in being right, telling everyone else they are wrong, and not considering any other views. Welcome to the Internet, human nature is exhibit #1... There is a quote about a million monkeys banging away on typewriters will eventually produce the complete works of Shakespeare. The Internet is proving that wrong.
Seriously though. I will say having played the whole trilogy 3-4 times, I can see any number of points where they were building towards the eventual climax. I see what they were trying to do. You have to consider that in discussing the ending. Was it perfect? No. Was the ending executed well? Not really (although the DLC helps somewhat). Let’s move past those questions. It is OKAY to have different ideas here.
(IMHO The biggest issue with the ending seems to be Casey Hudson – running around telling everybody in interviews that they could architect their own personal endings, setting the expectation that ME was not driving towards a specific end to the story arc. Doh!)
So what to do differently? I think the whole trilogy leads towards resolving the (supposedly inevitable) conflict between synthetic and organic for all time. Lots of ways to cop out on that. I mean it’s ambitious, and we can see a lot of players don’t like or accept the ramifications. The Reaper program was just the immediate ("we're gonna melt your ass down") symptom. There is more than just "blow up bad guys" going on here.
So a major point of contention seems to be: Any ending which does not address the big question is not adequate, and there are only so many ways to answer that. Lots of people pivot one way or another off this; I mean some face that and others avoid/reject it. I see narrow questions (like the appearance of Star Child vs. Harbinger as catalyst) as minor but interesting tweaks to consider. So we can discuss both smaller tweaks and The Big Picture.
(Original) Premise: the conflict is inevitable, lead to Reapers/cycle, which are practically unbeatable, to resolve that you will have to use some incredible power/hand of god to rewrite the rules.
Leads to Original Endings:
1- Synthesis. Is actually presaged by Saren, ME1 climax (after being made a cyborg by Sovereign) when he claims "I am the future- with all the benefits of both organic and synthetic and none of the flaws of either". Yes, Shepard dismisses this as a result of Indoctrination at the time- and NO I don't mean Saren was on the right track. Easy to overlook as it was so early, and I missed this the first time. Also, presaged with semi-cyborg Shepard (but they don't make it obvious).
(Lots of problems with this option if you question the 'hand of god' required to enact it galaxy-wide on ALL LIFE.)
RESULT: it joins the groups and circumvents the problem. "Understanding the enemy” will prevent future conflict. Arguable, but okay if you want to pick it.
2- Control. staged in ME2 obviously. Many reject the solution as “TIM is a bad guy" and thus this ending must be rejected by association. Or again, just a result of Indoctrination.
RESULT: It's valid, but sort of returns Reapers/Shepherds to their original role, right? Supercops. Supposedly that did not work out the first time, but with Shep guidance maybe this time... Ok.
3- Destroy. Remove immediate threat of the Reapers AND all Synthetics (for now).
RESULT: Punt. Just break out of the trap. The future can role the dice, i.e. Synthetics may/will rise again. Results in the most "freedom" but probably least long-term security.
... so I see those as valid at least, if you accepted the original premise. I mean they are some kind of answer to the big problem. I wish they had all been executed a bit better. None really guarantees a happy ending. Plenty of people hate when Hollywood falls back on the cheap happy ending in a film, right? So having framed why those are OK, I might add:
Alternative Premise: it isn't inevitable, synthetic and organic can combine forces and cooperate. Problem: means you have to save the geth to get there (removing play options/choices).
Leads to:
4- Total Alliance. Develop the Geth a little better (join Council, etc.). Synthetic and Organic Alliance plus a super-weapon forces a recalculation by the Reapers, who stop cycle program. Reapers stand down, go back to dark space and monitor (sort of their original mode).
RESULT: Reapers/Leviathans were wrong, show the conflict is not inevitable, and that the Reapers will listen. Shepard’s leadership is critical.
… sure there are problems with this one too. It may not satisfy either, and leaves tension. I am just saying it’s an alternative that seems to fit with the overall challenge and still has Shepard in a central role.
5- Alternate Destroy: Sort of the shields-down and Reapers blowed up real good… but leaves Geth/EDI unharmed. Again, it maybe avoids the primary conflict issue and is more a standard ending. But it could be a variation on the previous option too (if done right). It sounds like this would make more people happy.
Other options I can come up with reduce Shepard’s role... like Reaper factions (Prothean ghosts in the machine), etc. all simply side-step the primary critical issue. I am okay with Shepard sacrifice, however. Self-sacrifice is nearly always a compelling development and I didn’t expect Shep to live to see the Epilogue. The best epic heroes have tragic endings.
Really, I’m not offended if you have other ideas or preferences. I’d like to be respectful and consider them, maybe update my opinion, etc. if people can offer more than “UR stooped!”
So... I guess some arm waving should be expected. This is kind of like asking “If you could write the last 3 Star Wars films what would you do differently?” Flame on!