I havent read this whole thread, and I suspect my post will probably not get read by Bioware either, not surprising considering how many people think the ending should be changed and are willing to actively help get Mass Effect 3 back on the right track. At least, I suspect a large amount of what needs to be changed has already been explained.
Now, while I would LOVE TO BE, I am not responsible for writing the ending, so I will keep my response mostly in the realm of generic improvements.
The way I see it, we are limited to two paths here: Retcon the current ending (preferrably with some kind of logical plot device like Indoctrination) or keep the current endings, but give some explanation , because right now the plot holes are enormous (its also not satisfying wondering what happened to your crew; this is the lesser of the two optons, imo).
So, if you go with the latter option, there isnt much for me to help you with, cause you already know what needs to be done. Basically, add a fourth option, where he says, "Right now, salarians and krogans are standing side by side, geth and quarians are fighting and dieing together to defy you. We'll take our chances, and I promise, someday, Synthetics and Organics will stand side by side on your grave's" to the catalyst (harbinger

).
With the former option, where the on disc ending is retconned, the sky is pretty much the limit. But what I basically want to see is:
1) The war assets I gained/ missions I completed/ allies I brought together DOING SOMETHING. I want to know the Rachni munched up a brute, I want to know the Krogan stopped the reapers just befor they killed a squad of humans, I want to see the Geth holding the line while quarians hack reapers. I want to know the ASSETS MATTERED. I will add to this, that I want to see where all my choices lead, what their final impact was.
2) I dont personally mind two of the ending choices being "Do you want to control the reapers?" or "Do you want to destroy the reapers?", but I DONT want to see the catalyst, AT ALL. He came out of nowhere, and acknowledges he is your enemy, but you have to listen to him? Those choices should be on Shepard alone, if theyre there at all. And when I destroy the reapers, its ok if Shepard has to die, but have it so he destroys the reapers and dies a hero and all that he did ISNT ERASED, so, the Turians and Krogan REMAIN ALLIES, the Relays arent destroyed so the peace you garnered WASNT A WASTE. I will get back to how epilogues, and ending cinematics should look. And If I choose to control the reapers, maybe I live, but at the cost of my humanity, imply that I may be the next threat to the galaxy. OR, show the humans ruling the other species in the galaxy, with shepard as the militant Dictator, leading a REAPER ARMADA! Come on! I would play through to get that ending once. THINK KOTOR (you know, your best game to date). And why not throw in better and worse endings, in all varieties, based on how well I played. Make the "PERFECT" ending actually perfect.
3) Write a story for what happens after. This one is so important. Show Ashley with our son looking at my memorial. Show Garrus, still holding the line, commanding his own ship (where somebody is surely making calibrations). Show the Geth and Quarians rebuilding together. Show Javik coming to terms, saying "Enough people died Shepard, so I will become the new carrier of memories, and I will live." DO THAT! MAKE ME SHED MAN TEARS AT ALL THAT BIOWARE AND I ACCOMPLISHED TOGETHER! Make it bittersweet, sure, but not by making it confusing, or erasing all the good we did along the way. The epilogue was ok, but it didnt feel connected to any ending, it felt tacked on. Right notw, its like a generic Sci-Fi Epilogue that feels out of place.
4) BY MARAUDER SHIELDS FIX THE PLOT HOLES! This is the worst part! My team couldnt suddenly appear on the Normandy. WHY DID JOKER FLEE EVEN BEFORE I SET OFF THE CRUCIBLE? Etc etc (im sure youve seen the articles that put them all out there)
5) Spend some time on it, dont just rush it. Right now, the ending even FEELS incomplete. No voice acting? Everything else was so High Quality! It really feels like a place holder ending.
6) The "Buy DLC" message seems heavy handed, and is truly offensive with how things stand. I thought the "One more story my sweet" at the end was an in-universe ad that was much classier. Do something like that, or have Shepard (or whoever is still alive) say, "One more mission, for old time sake" cut to black. Something like that.
7) Either dont fully explain the Reapers motives, or come up with a much better explanation. The current one is hypocritical and a little... lackluster. There was a time early on where I thought Reapers were technology and resource farmers (letting civilization reach its apex and then "Reaping" it), thats a pretty simple and basic explanation. We would just be resources to such an advanced race. OR, have their motivation be fear, fear that one day another civilization will reach a point technologically where it was a threat to even them, and so they nip it off at the root before it gets there. Then, they make altruistic claims to mislead Shepard (like the catalyst). This is a place you have somewhat worked yourself into a corner, it will take a very creative mind to come up with something completely satisfactory, so good luck.
8) STICK TO THE ESTABLISHED THEMES! Extremely important here. Up to a point, the biggest difference between renegade and paragon options has/had always been that one was pro- diversity and one was pro-humanity superiority. So, the most important thing below stopping the reapers, was either achieving Human dominance, or harmony between the species. Basically, it was all about the two sides to acceptance (pro or against). And this game was even MORE focused on this theme! You put to rest ancient conflicts OR you dont and you help one side get a foothold over the other! Krogans and Salarians. Geth and Quarians. The finale should REFLECT THOSE THEMES! And I the saddest thing is, I think you guys actually tried and dropped the ball, but it is so simple. Give shepard the option, while defeating the reapers, to either make humans the dominant race, or to leave the status quo in tact! It felt like you were building toward this the whole time, with the councils shenangans and all.This would appeal to all types of people, and would add replayability for at least a second run. Imagine, the humans come out of the cacophony, with NEW FOUND POWER, leading the greatest fleet the galaxy has ever seen, taking the lead in galactic matters. OR, everyone working together to rebuild, allies, at least until the next political squabble. Both have pros and cons, which makes both interesting.
9) Make our final choices matter as well. Dont let the game end the same whether you choose A, B, C, D, E, F, or G. Make each one completely unique. If theres an ending where everyone aboard the Normandy dies in a blaze of glory, getting a newly discovered system dedicated to them ("Because they gave us a future, and were always the light which lead us through the darkness, we will christen this star, THE NORMANDY") AND an ending where we see the final moments with Joker dodging amongst Reapers, a huge flash, cut to black, then a Sunny beach, with the entire crew having a beach volleyball contest, AWESOME, MORE VARIETY

.
I think thats everything, for now.