The ending to Mass Effect 3 is fundamentally, fatally, flawed. Barring a complete rewrite, it cannot be fixed, and will never rise to the standard of a good ending, let alone a great one.
That being said, the Extended Cut is a vast improvement over the previous ending. This ending is significantly stronger, and significantly more cohesive. The Extended Cut is still a poor ending, and is not the ending the Mass Effect series deserves. But it is better than the absolute travesty that preceded it.
(Spoilers below the cut!)
There are two major strengths of the Extended Cut.
First, it cleans up a lot of the unanswered questions surrounding the Choice that were alluded to. Why was the Normandy escaping? How did your comrades on the ground get on the ship? How do you control the Reapers when you are dead? The reasons given are good enough.
It also clarifies who the starchild is, making it pretty clear that its an AI that went rogue and turned on its creators. Why we now trust it to elucidate our choices is not clear, but I guess we just run with it.
The other strength is that it clarifies the aftermath of the Choice, showing what happens to the galaxy and your comrades after your choice. They also got rid of that silly "Into Eden" ending, making it obvious that it was just temporary, rather than a cliche.
The weakness of the Extended Cut is the same as the original ending of Mass Effect 3: the Choice at the top of the Citadel.
I started detailing this weakness, but it got very long, so I'll turn it into a separate post. But basically, if you were unhappy with the Choice before, I expect that you will be unhappy with the Choice now.
One minor change I noticed is that during the Battle for Earth there's a sequence where a civilian radios in for help and a medic walks her through bandaging a wounded soldier. In my original game, the civilian failed to save the soldier. Then when a husk approached she took the soldier's gun and commits suicide rather than suffer being harvested. It was quite tragic and shocking, especially as it was purely done over the radio/phone. But in the new play-through, the civilian saves the soldier, and everything works out. I'm not sure if this is an actual change, or if it's a consequence of the lower EMS ratings needed for the "best" endings.
Sadly, they didn't change The Illusive Man confrontation. It's still the impossible Paragon conversation option and double Renegade actions.
There is one new ending: Refusal. If you refuse to make a choice--or if you are like me and Azuriel, you shoot the starchild in the head at the first opportunity--a new ending triggers. In this ending the Reapers win and wipe out everyone. But the information Liara leaves behind allows the next cycle to defeat the Reapers once and for all. Possibly because Liara leaves better clues than the Protheans.
This is actually a really good ending. It makes sense in terms of what came before. It is a real consequence of your choices. The only bad thing about this ending is to get it you have to deliberately spurn the "real" choices, deliberately condemn everyone to death. If this ending had been unavoidable, maybe if your EMS rating was too low, it would have been a solid option.
Of the aftermaths, in my opinion, the best one is Control. Shepard as the Ascended God-Queen of the galaxy, guarding if Paragon, ruling if Renegade. It's totally in character, and so very Dune.
The aftermaths are all well done, and worth seeing.
Finally, baby Krogans! I'm pretty sure this whole kerfluffle was worth it for that one slide.
The weakness of the Extended Cut is the same as the original ending of Mass Effect 3: the Choice at the top of the Citadel. But everything around that Choice has been made as strong as it could be. A lot of the questions surrounding the ending have been fleshed out and answered. The ending is stronger and more cohesive for this.
But the Choice is still a gaping wound. A fatal weakness.
If the original ending was an F, I would say that this ending drags that up to a C.
However, Mass Effect is arguably the seminal science fiction work of the last decade, and it is extremely unfortunate that the ending does not live up to the rest of the series.