I have read many wonderful ideas and I'd like to contribute one of my own as well. In addition to being epic and answers more questions, I also want to make it really
practical so Bioware might just do it.
Section 1: In the Cerberus base:
* Adding a cut scene or a video log about Cerberus researching into the origin of the keepers. They were among the earliest indoctrinated species by the reapers until they become completely mechanical, and their goal was programmed to hide the true purpose of the Citadel from its residents (a mass relay allowing reapers to return.) Remind us here that Protheans unlocked the secret of keepers in the end of their years.
* The Illusive Man's biography was unlocked as Shepard travels deeper into the station (can be done with pda or video logs), and finally accessing Illusive Man's early experience as Jack Harper unlocks a greater secret: The Reapers' winning technique in each cycle was to pit organic life against each other until evolution advantage decides who's winner, then they come to defeat one species that has become too isolated to have the same weakness (Just like Jarvik said the weakness of protheans was a lack of diversity.) Therefore, one of Sovereign's jobs was to create an "upraiser" in each major species by indoctrination, and the "upraiser" will pit his own race against others by xenophobia, hence Cerberus is born. In the turians Saren was the upraiser, and in humans it's Jack Harper. But since Sovereign was destroyed in the end of ME1, Illusive Man no longer receives "not fighting reapers" order and began to genuinely fight against the reapers for the sake of humanity. This explained why he was rather eager in ME2. But in ME3 when Reaper fleet returns, he entered the range of the massive indoctrination fields around the reapers and became indoctrinated and therefore deluded till the end.
Section 2: Fight on Earth
This part does not need too much fix. If possible, I personally would really like it to be similar to the ending mission of ME2 in which Shepard assigns teammates and ground forces to do different tasks, and his assignments has results on the survival of squad mates. At least, Shepard's entire squad should be all involved instead of only 3 people.
Section 3: Beam to the Citadel
This is probably the part that requires the most fixes.
* Instead of being hit by reaper laser, Shepard was beamed to the Citadel intact. This is the ganrantee for any future combats.
* Shepard arrived at the dark unknown area in the Citadel. He found out that the area was where the keepers come from endlessly - they are constantly being reproduced from melted organics reapers harvested from the last cycle, and they simply don't run out till reaper's next return. Among them there are considerable amount of Prothean memory logs, but Shepard can understand them due to ME1's cipher.
Recall in ME1 on Ilos, Vigil told us that a small number of Prothean scientists were sent to the Citadel after they built the conduit, but their endings were unknown. Now their endings are known - they spent their last moments studying how the Citadel manage to open channel to dark space without ever being detected in normal days. It's because Citadel was built to have the ability to concentrate dark energy - it diverges it to the vast space nearby so not to cause detection, but when reaper returns, it can concentrate dark enery to form a path between it and dark space where the reapers dwell. This discovery made the Protheans realize that the Citadel was the missing Catalyst they have been looking for - a super-structure that can concentrate dark energy as said in game. They recorded it with their memory logs and sent the signal off world before they died.
* I suggest a battle level inserted here.
* Confrontation against the Illusive Man with Anderson doesn't need to be changed much, although Illusive Man should have some fighting skills now that Shepard is healthy (actually he can fight for sure as in the novels). I find it a nice piece of game just before the final boss fight to enjoy the view of Earth with the dying Anderson.
* Instead of being somewhat automatically sent to the upper Citadel, Shepard activated the flying platform himself after radio contact about the Crucible not working. Squad mates should be all aboard the Normandy by now, preparing for a final assult in case Shepard fails to activate the Crucible.
* On the upper level Citadel, instead of talking to the out-of-nowhere child holograph, Shepard finally confronts Harbinger who has realized the whole Crucible plan and flies here to stop Shepard. They had a brief conversation before the fight starts.
The main philosophy behind the conversation between Shepard and Harbinger should be this:
The reapers seek to end the chaos of organic life with a perfect unity by making them all into reapers, since organic life inevitably go into conflicts. By pitting organics against each other, reapers purifies the strongest, and then make them into reapers to end their chaotic nature forever and become immortal.
Shepard argued that: In spite of the chaos, the fact that Shepard brings the whole galaxy in union against the common threat has proved that organics or even synthetics CAN live in cooperation and WILL help each other. The galaxy can co-exist with different races and such diversity will be the downfall of reapers this time. (Such is the theme thoughout the Mass Effect universe, and it's a rather emphasized one.)
* Final boss fight with Harbinger began! In my mind it should be somehow similar to the reaper fight on Rannoch, just Shepard has to also deal with reaper minions this time, and Harbinger is destroying the Crucible so there's a time limit. The details are for the gameplay team to decide.
* Finally, Harbinger is defeated and the Crucible fires a huge pulse that announced the downfall of all reapers. The pulse travelled through mass relays (but not destroying them) that purged the galaxy of reapers. It does not kill organics so Shepard and the rest of the galaxy is fine.
Harbinger's last words were these: "Shepard. I have realized the power of your primitive organics. Though negligible and finite, in unity you demonstrated a cohesiveness none of the former cycles have experienced. Your galaxy shall please the Grand ones. We have come to secure the order over organic chaos, and we have witnessed the order and unity today. Our purpose is fulfilled."
Then he explodes.
* Soldiers on every planet cheered, and Shepard was rescued by Normandy.
Ending scene:
* Right after the war ends:
The alliance conference hall was flooded by reporters - led by Diana Allers - when Shepard was to give a speech. Shepard can choose to emphasize on the importance of humans or importance of diversity. Afterwards Shepard can talk to each of his friends in the hall to comment on their future life as well as Shepard's. Just like the ending of DAO. I personally find this type of "mass friend" ending very tear-driving in a good way. The choices Shepard makes here about his own life will affect the post-ending slide.
In the end of the guest addressings, Shepard reports to Admiral Hackett, discussing whom the "Grand ones" in Harbinger's speech were referring to (open possibility to the future ME universe). But that will be up to people of generations later when humanity steps deeper into the vast universe. Shepard's tale ends with a historical victory.
* Slide show:
I fully expect a detailed ending slide show featuring how our every dicision has affected the galaxy as a whole. With closure of all previous choices and romances as well as all our friends,squad mates, planets and projects.
* Post slide:
Shepard get to make a conclusion to his advanture based on his earlier choice in the alliance hall, and of course, with his love interest, devoted to a new life together (if s/he has one).
*Ending credits* and No stargazers.
The reasons why I think it's a good idea:
1. It answers some of the unsolved major questions, such as Illusive Man's true shape; the result of the Protheans on Citadel; keepers' identity; Why Citadel is the Catalyst...etc. without bringing a lot of foreign contents. All my story tellings above were based on passed ME1 and ME2 events.
2. I love past-story-referrences and I think many royal ME fans like them too. It makes me feel connected to the passed games while playing a new one.
3. It does not require nearly as much work as some of the more fancy ideas. There is not even one extra map needed. All needed was extensions of current maps with some more voice casting and animations of already-existed models. There are granted more combat scenes, but I guess those are not too hard to make compared to adding a new level. I really tried to keep the original game in one piece as much as possible.
4. It shows an epic and brighter ending with the consequences of our past choiced shown to some degree. It is not completely Disney-like either.
5. It has a somewhat consistent philosophical line.
I spent quite some work on this ending. Please share thoughts

And thank you for reading.