My suggestion: Fix the main problems with the Reapers. Honestly, I would have done that end sequence lot quite differently, but seeing as its what we've got, and what you have to work with, I'll expand upon it to try and fix these problems:
-Plot Holes
-Reaper Logic not being logical at all, and making 0 sense overall
-No reasonably happy ending to the Epic of Commander Shepard
-No reflection of choices
-Lack of diverse endings
and maybe a couple of others too.
Lets start at the beginning of the end. It is all very homogeneous. No matter what, the scene barely changes. Yeah, there are a couple of differences, but nothing that really reflects what we've done. Actually, two things that somewhat reflects what we've done: The Destiny Ascension and the Geth/Quarians.
Now, how to improve this? Well, it will take some work to make enough cutscenes and implement them, but not too much considering that all they really are are cutscenes.
What we need is a greater reflection of our decisions. Rather than the same start except a couple of different ships, show each fleet jumping in Individually. I'm talking each race's fleet. In this case, also include the Salarians. Sure, we didn't get all their ships if we saved Wrex and cured the Genophage, but we did get at least one.
At the minimum, these fleets should be shown jumping in (First three can be shown as is in game, as they are always there):
-Alliance
-Turian
-Asari
-Salarian
-Quarian/Geth/Both (If Both were saved, show each fleet jumping in separately, or a joined fleet of the two jumping in together)
Now, there isn't a lot here that really needs doing. You have the Alliance, Turians and Asari, as well as individual jump ins for both the Quarians and Geth. What is needed now is to allow for both cutscene portions with the Quarians and Geth to play, and add in the Salarian fleet entering. There shouldn't be any sync issues with music or the likes as, really, there is no music (None was playing for me at least). It gave an ominous feeling to the battle, and works to your advantage here as without music to have to sync the scene to - your free to add in more as you wish.
Next, improving the battle itself. Most of it plays out rather homogeneously, except for a few minor details. Keep all this in game, but also show the results of some of our choices.
Say you saved the Destiny Ascension and the Geth, show a scene with the Destiny ascension engaging a Reaper Capital Ship, and as its about to get shot by it, a Geth Dreadnought flies in the way of the beam, sacrificing itself for the ship its kind tried to destroy 2 games ago.
Show the Salarian fleet engaging the Reapers, different scenes dependent on if you got their full support, or only partial. I want to see their Thanix canons firing though. Damaging Reapers a lot, then they either get swarmed and take some damage if you didn't get all their fleets, or their fleets hold their own against the Reapers if you did.
Show Quarian Liveships and Geth cruisers engaging Reapers, either individually, or both at once (Dependent on choices).
Hell, if you really want to show some details, Have the ships you recover from planet scanning shown in their own cutscenes too: The Agincourt, the Shanghai, ect.
Show the Normandy engaging. If it has a Thanix canon, fire it. Do something similar to ME2 attack on the Collector base for the Normandy, so your choices then affect even now.
Show the Volus Bombing Fleet attacking Reapers, if you acquired it.
Make the player feel as if they made a difference to the fight.
A few extra assets to create, but it would vastly improve the 'Sword' fight alone. If you want the maximum effect, a lot of extra assets will need to be created to showcase all of the players choices that influence the sword fight. You could get away without showing many of the minor ones though, so long as you show at least some of the choices they made taking effect.
Next, we'll move onto the ground 'Hammer' Operation. This doesn't need as much cutscene overhaul, but it would be nice to have some extra models made for some of the fights, and extra dialogue would likely be needed.
As stated by G3n0c1de here:
http://social.biowar...13/134#10238022
have the FOB be in a different situation dependent on how well Shepard prepared the ground forces. Cutscenes could be used to easily convey some of this, but a better effect would be to have it play into the missions in that area.
Have Kirahe do another of his 'Hold the Line' speeches, the one in ME1 was epic.
If you have Krogan support, have some of them around in some missions, fighting with Shepard in certain areas.
If you have the Merc support, show them fighting too.
You got those Geth Primes? Have them do Orbital Drops in at one point and start fighting for Shepard.
Not only does this reflect player choices, but it also influences the gameplay somewhat so that these choices have meaning.
As stated for 'Sword', just how many of the players choices that would affect 'Hammer' you want to include is up to you, and will affect how many (If any) resources you need to add to the game, but things like having the Biotic students with Jack either providing support for some Marines that support Shepard, or acting as Artillery for him if Shepard chose that, or seeing the Zhu's Hope colonists charge into Battle, and act as a single unit thanks to Shepard saving Shialla and getting them the cure or W/E, would really count towards the player feeling engaged in the fight.
As an added bonus, this also engages the players more with the assets they've gained. They may have grown attached to those Biotic Students, and if they enter the fight, some Shepard's may go out of their way to protect the Biotics, or the Krogan, or anyone they gathered and know on the ground.
Now on to the Conduit Rush, and the Citadel. This is is where I'll change a bit from G3n0c1de.
Keep the Missile launch section the same, but have that final run to the Conduit influenced by assets as well. Show some of Shepard's assets trying to make it through. Keep the rest of it largely the same, but instead of the beam directly hitting Shepard, use it like in the intro for the game: The Beams don't hit him, but the shockwave knocks him over and hurts him. Then have Coates say everyone was wiped out, but have people question "What about Shepard?", to which Coates replies that he doesn't know.
When on the Citadel, the Illusive man mind battle can play out much like it did, but revert the speech with Anderson to that other version I've seen floating around. Once Anderson loses consciousness, don't have Shepard lose consciousness too. Have Hackett contact him about the Crucible not firing, and Shepard goes to activate it. At that point, Harbinger floats down in front of Shepard. Now the true battle of wills begins.
The Catalyst child thing no longer exists, instead the Citadel itself is the Catalyst and fires the Crucible. To represent the Reapers: Harbinger. The Antagonist from ME2 till now, we will finally get a resolution to him.
Firstly, Shepard stands 0 chance against Harbinger in a conventional battle, so they have a battle of wills. Harbinger explains the Reaper's reasons for wiping out Organic life, and rather than simply 'Synthetics will do it if we don't', add more to it than that.
For one, have the whole synthetics problem. If Shepard allied the Geth (Quarians are optional, though not required as all that needs showing is that synthetics and Organics can work together), they can convince Harbinger that synthetics don't have to live at war with Organics. Otherwise, we move on to another ending (This whole thing leads up to one ending).
For two, have the 'younger species' argument, where the older species are wiped out to make room for the younger ones. If a Shepard knows their lore, they can argue that the council races have taken care of the Younger races. Harbinger will ask for proof of this. Shepard is given three options with whom to respond: The Krogan, the Yahg or that Bird race that knocked all its satellites out of Orbit and that so the Reaper's wouldn't harvest them. Picking the Krogan causes Harbinger to point out the consequences of ascending the Krogan, including their eventual slow demise by the Genophage. If the Genophage is cured and Wrex is leading the Krogan, Shepard can use these as evidence of how Organics can fix their past mistakes in those regards, and Harbinger will accept it. Otherwise, other ending.
Picking the Yahg will result in Harbinger bringing up how the Yahg aren't even ascended, and how the only reason that Organics stay away from their planet is because they are afraid of the Yagh. He may even point out the whole Shadow Broker debucle. In the end, this option means another ending is required.
Picking that bird race will lead to Harbinger saying that they are a pre spaceflight species, and asking what Organics would do once they were ascended to spacedom. Shepard responds that the are a spaceflight species, and the Council has already made first contact and accepted them into the community. Harbinger checks Citadel records and finds this to be true, allowing this ending to continue.
The final argument to be had with Harbinger is about the risk Organics pose to themselves and each other, citing cases such as the Krogan rebellions, the Krogan treatment of their homeworld, and the Rachni. Shepard is given some options to Argue.
If he argues that Harbinger is only pointing out flaws in the Krogan, and that if they're the ones the Reaper's have problems with then they're the ones the Reapers should be fighting, Harbinger points out how quick Shepard was to backstab the Krogan, and the option for this ending is lost.
If Shepard saved the Rachni, he can argue this point to Harbinger, and how it shows that Organics will also help each other recover, not just wipe each other out. Harbinger will accept this and the ending is unlocked.
If Shepard spared the Quarians, he can argue how Organics stood beside other Organics against the threats posed by the Synthetics, and how they overcame this difficulty, eventually resulting in peace and life for all (Seeing as you would only get this far by saving the Geth anyway, it is safe to assume that both the Geth and the Quarians would be alive for this). Harbinger accepts this as well, and this ending is unlocked.
The ending I have been talking about is an alternate to control. Harbinger sends out a pulse to the Reapers. It travels through the Mass Relays to all Reapers in the Galaxy, and behaves similarly to the 'Control' Ending cinematic (Minus Relay Destruction). The Reapers stop fighting, and Harbinger tells Shepard that the Reapers will go to a place where they will not be found, but they will be watching, and will return if the situation demands it. Everyone is saved as Shepard managed to talk down a Reaper, and make peace between everyone. Shepard passes out, then the Epilogue occurs (More on this later).
If Shepard is unable to carry out the above task, Harbinger beings to charge his Beam, and Shepard has a few moments to use an Interrupt.
If they use the Interrupt, he runs up and activates the Crucible. It fires and Harbinger is Obliterated. The power from it firing sends Shockwaves throughout all the Mass Relays, destroying them and all the Reapers. It plays out a lot like the Destroy ending, though the Citadel remains in tact. Shepard then passes out.
If they do not use the Interrupt, Harbinger Fires into the room, killing Shepard and Destroying the Crucible.
If Shepard's EMS is high enough, his allies still win the battle, and everything is still intact. Sadly, Shepard is dead.
If Shepard's EMS is not high enough, his allies lose the battle, and the Reaper's win the war - and go on to harvest all life in the galaxy.
Finally, the Epilogue. Unless Shepard died AND the Reapers won, the Epilogue should follow this sort of structure:
-Shepard themself. If they fell unconscious rather than dying (Talked down Harbinger or used interrupt to fire Catalyst), it tells of the Normandy flying Hackett to the Citadel, and them finding Shepard and Anderson, and TIM, and collecting them up. Shepard recovered under Doctor Chakwas' supervision (And Mordin if alive [It is possible to keep him alive right?]). From there, give them an epilogue based off their LI, and whether they were Paragon, Renegade or Both.
-Anderson's fate. Explain what happened to him, hopefully with varied outcomes based off different variables.
-Earth's fate. What happened to Earth after Shepard's actions?
-Normandy's fate: What happened to the ship. Was it damaged badly in the fight, and needed to be junked, or refit again, or did it survive well through the fight?
-Tuchanka. What effect Did Shepard's actions have one Tuchanka
-Rannoch. If Shepard killed the Quarians, kept the Geth, show the Geth Retreating into the veil again. If he killed the Geth, spared the Quarians, show the Quarian's rebuilding alone on Rannoch. If he saved both, show both rebuilding on Rannoch.
-The Citadel. How did things play out on the Citadel for Bailey and that? Did they find a place to survive? DId they use Cerberus's turrets to defend themselves?
-Fates of Thessia, Palaven and the Citadel races in general.
-Fates of Each Individual Squadmate from all three games
-Fates of important characters that weren't squadmates, such as Aria, from all three games.
-Fate of the Relays
-What happened with the Reapers, and if they lived and hid, did they ever show signs of returning (Certain choices maybe caused them to want to return).
Hopefully that would fix the issues I listed above, without too much extra work (Well, a lot of optional work, minimalist work is still a bit, but shouldn't be substantially more than any other DLC I wouldn't think).
Now, this is largely a rewrite of the whole ending sequence, which I understand you are unlikely to do. It is what I would like you to do, but I understand that it would make it difficult to charge for it as it would divide the player base. As such, at the very least include the improvements to the 'Sword' and 'Hammer' battles, and the Epilogue. Preferably include all, or your own version of all, in the DLC, as an 'Alternate ending pack' that can be turned on and off in options. Something like this would make a lot of people a lot happier.