Just played the game again and suffered the ending ... the pain doesn't stop! Bioware obviously has very talented writers, but they must have been excluded from the ending part, which was written by the big names in the credits (they pulled a 'George Lucas').
With that obligatory gripe out of the way, here's what I feel needs to be here (maybe Bioware will learn from this mistake or a kind soul will create a mod, or a fan-made graphic novel):
There needs to be some detail on how the Reapers take control of the Citadel and get it to Earth. Sovereign wasn't able to do this without Saren physically taking control of the Presidium Tower and accessing the controls. The easiest explanation would be that the earlier Cerberus attack was a cover to install some insidious Reaper-based code into the Citadel control which would override all security. The Illusive Man would have done this in order to sabotage the Citadel and allow the Reapers to interact directly with it, with the idea of sweeping in and taking control of the Reapers using the Catalyst in turn (of course he is deluded and was acting under indoctrination).
A cutscene showing the Reapers warping into the system, and C-Sec officers panicking as they lose control of the Citadel systems would be enough. A deck officer could make a comment like: 'Cerberus must have uploaded a Reaper virus during the attack - warn the Council, we've lost access to the Citadel controls'.
Depending on Shepherd's efforts to build up Citadel security preparedness, the Reaper forces attack and we see scenes of civil and C-Sec resistance in the streets (or a massacre if preparedness level is too low). Some small Cerberus ships, commanded by the Illusive Man, could be seen dodging the chaos and fighting between the Reapers and the Citadel fleet, to dock with the Citadel.
Either way, while fighting rages, Harbinger docks with the Citadel (much as Sovereign did before) and the arms then close - the Citadel and escorting Reapers then warp out of the system and warp into Earth space, where hundreds of Reapers are massing. A small relay can then be revealed in London (much like the Ilos one), where Reaper forces herd prisoners (maybe in cocoons like in ME2). They are being sent up to the Citadel where players can imagine they are being 'liquified' in preparation for a new Reaper to be made.
The rest of the plot-line can take place as is, with Shep and company fighting their way through London to get to this mini Relay. We do need to see more examples of races fighting on the ground (not just 16 Krogan standing on parade). We need to see Geth and Quarian marines fighting side by side, Krogans swarming over rubble to help some Turians from being overwhelmed, some Asari Commandos fighting with humans. There needs to be a sense of the whole galaxy fighting side by side, not a human battle with a few token aliens on the sidelines. The space battle gave some sense of this, but not the ground battle.
Needless to say, Harbinger (being docked with the Citadel) will not appear, although it should be quite a challenge to get to the Relay - maybe even with two smaller Reapers backing up lots of Reaper ground troops (similar to the one guarding the Spire on Tuchanka) - Wrex could even make a comment like 'wish we had a couple of Thresher Maws with us now'...
The Normandy should drop off the rest of Shep's team just before the final assault, and then fly interference for the ground forces during the attack - with Joker pulling some insane pilot manoeuvres. The final attack then begins on the Relay.
After winning through to the base of the London Relay, Shepherd could be cut off from other allied ground forces by a counterattack of vast hordes of Reaper ground forces. Anderson could call out - 'we'll hold them, just get to the Relay, Shepherd!' - and then carry out a heroic holding action with what is left of his forces. Another nice scene for small bands from different races saving each other and fighting back to back (maybe even the Rachni could swarm in at one point to save some Krogan!)
Shep and his team should be the only ones who get through the Relay and land on the Citadel (on the Presidium where the mini-relay previously linked to Ilos was) - this would be a nostalgic reference back to ME1 scenery. As in ME1, it is mostly blocked and the team has to detour and fight through the streets (combat in a ruined Silversun Strip would be fun). They should come across other characters still resisting the Reapers - Commander Bailey and some C-Sec grunts, Aria and her mercs, Some civilians, etc. Shepherd will have to assign members of his/her team to assist the different groups, like in the Collector Base in ME2 (3 squad members to back up Bailey as he tries to take back C-Sec HQ, another 3 to help Aria save a group of trapped civilians, etc). Eventually, Shep will be left with only 2 companions who will accompany him/her into the Tower where they will find a final scene (maybe a ruined High Council chamber - maybe a previously concealed chamber at the heart of the Tower, where the new Reaper is being assembled). There s/he will run smack bang into the Illusive Man and his last surviving henchmen. Shep's companions can hold off more Cerberus henchmen while Shep personally confronts the Illusive Man in a scene not unlike the one currently. Shep can still be injured at this point, but obviously without Anderson. Maybe Shep's 'love interest' (captured just before - 'sorry Shep, he took me by surprise ...') could be the one held hostage by the Illusive Man - making resistance that much more risky.
After overcoming him, Shep accesses the controls, opens the arms, allowing the Crucible to dock, and gets up to the Master Control area where he is confronted by the Catalyst intelligence. The Catalyst can appear as the kid, or shift through multiple shapes (like the Leviathan did when it communicated with Shep), but eventually it should reveal itself as an avatar of the Citadel itself (recommended: Avina - the guide that has appeared all over the citadel from the beginning). The 'Avina Avatar' would be essentially an AI in control of the Reapers but lacking full control of the Citadel, thanks to the Prothean scientists who sabotaged it previously (ME1).
The final choices can be offered to Shep, but need to be re-written and waaaaay less confusing and disjointed. The 'Green' choice of symbiotic integration between organics and machines should be dumped (it makes no sense to anyone). The choices can be between 'control' - which is an 'indoctrination' ending where, if Shep falls for it, will be indoctrinated, and the 'pruning' of organic races will continue ('assuming direct control ...'). A very 'civilised' Yog archaeologist could come across Liara's recording in a 'future-time' cutscene 50,000 years in the future. The second choice would be destruction, which should release energy waves via the Relay network (not blowing them up!) but causing huge damage to technology (damaging the Citadel and nearby ships), causing Reapers to self-destruct, and basically kicking off a Galactic dark age - but at least organic races would survive, and technology could slowly be repaired or rebuilt. A really sad scene of Joker bending over a dying Edi would add a good emotional hook. The third choice should be 'sacrifice' which should cause a feedback loop between and Citadel (catalyst) and the Crucible, blow out part of the Citadel itself, destroying the master control section and the Catalyst and crippling the Reapers, which become inert, while not damaging other technology, but this one would result in Shepherd being killed in the explosion (despite efforts by his/her injured love interest or companions to save him - a nice emotionally jerking scene here to bring some tears ...). A low preparedness score would result in more of the team members and other characters on the Citadel dying along with Shepherd. It would probably be a good idea to have a 4th option too (to get away from the typical 3-option ending), and that would be some kind of delaying tactic, whereby Shepherd threatens to destroy the Reapers if they do not withdraw - this would need an absolute max out in either Paragon or Renegade scores. The catalyst intelligence would then download itself into Sovereign and bug-out, along with the rest of the Reapers, to fight again another day (once they've adapted their defences to withstand the Crucible). The galaxy would still be under threat against their implied return in 50,000 years, but it would be the least destructive ending. It would also allow for the 'Yog' archaeologist scene ...
Preparedness levels and players' choices would then impact on the aftermath regarding who died and who lived, what condition the planets were in, etc. Scenes of Citadel cleanup or ruin, the raising of a monument to Shepherd on the Presidium (if he didn't survive), scenes of vast destruction of planets if preparedness levels were too low, etc.
This is a long rambling post - but maybe someone will enjoy the train of thought here, and add to it even.