I'm having the same bug that everyone's been having, IE when Miraak goes ethereal, I absorb a dragon soul instead of him, and the quest can't progress further. All solutions I have found do not work for me.
So my question is: Is there any way to progress through this with console commands? I'm sick of fighting Miraak and just want this damn thing to be over already.

A bit more info:
I can use resurrect to get him to at least the second dragon, but after that, he'll try and absorb the soul of a dragon that's already dead.

Dude, not 'everyone' is having your problem!
The Miraak fight works flawlessly...
Unfortunately though, it takes only 30 seconds (because Miraak is an enormous wimp).

So I dunno... I guess your game is buggered up?
You wouldn't be running a huge bunch of mods would you?
What about all the patches - the Unofficial Skyrim, Dawnguard, Hearthfire, and Dragonborn patches?

In 1200 hours playing Skyrim, I have never opened the console - not once!
Maybe 'everyone' with your same problem has buggered their savegame as well?
No. And in fact the question itself is very unfortunate.

I've seen and talked to tons of people, across both Xbox and PC, with the same problem I've been having. This is a very common, and very known bug. So yeah, they are.
If you're not gonna help me on something and instead just rag about how it's my fault, can you just... not post? Please?

Nother update, killed all the dragons before attacking Miraak, now he just sits in his kiddie pool, looking at me sadly because he has no dragon friends. Still won't absorb the souls of dragons.

This thread solved the problem: http://www.gamesas.com/topic/1443929-bag-with-invulnerable-miraak-solved/

Just be sure to follow the instructions EXACTLY, it's tricky.

Just have to say, Bethesda has been absolutely NO help on this issue. It's despicable that they let a game breaking bug continue for so long without a hotfix that the fans had to do it themselves.

Again, shame on you bethesda.

Already did that, didn't work.
Eventually just opened up the CK and reworked Miraak's script to bypass any sort of dragon-soul-svcking, which worked fine.

I would sincerely appreciate a detailed description on how you did that Trainwiz (not familiar at all with the Creation kit) as I am having the exact same problem with Miraak.
Trying the above mentioned solutions did not work for me either.

Does anyone have a solution for this?

I've tried the console commands, but I can't leave Apocrypha due to the dragons. I can't use console commands to kill the dragons, but they keep me in combat.

How long I take to defeat Miraak the first time seems to have no relation at all to whether he gets stuck in ethereal form. If I do get past the first ethereal bit, then he simply vanishes from the map, which also stops the fight from progressing. All of these are bugs described by people using XBox and PC without mods. They're listed on UESP as known bugs.

Did find a command to advance things to remove the dragons, but now I'm stuck with unending battle music and I can't find a way to change it. Actually fighting dragons or other monsters doesn't do anything. With dragons, the music stops briefly but starts right back up.

https://mega.co.nz/#!1UMiSbZD!flHPiDnSnSDMvBuRXoB6JCuOnYVoUOoelZXYfQruuvw's the modified version of his fight script, which you could use. All it does is skip over the dragon absorb parts, and go straight to his death scene.

Thanks much.

It doesn't clear the dragons, which leaves you in combat. The book won't allow you to use it while in combat.

To clear the dragons, open the console (~) and type

setstage dlc2mq06 600

If the combat music does not stop, apparently this will remove it:

removemusic dlc2muscombatboss

If you really need the three additional dragonsouls that Miraak would have given you if he'd absorbed the souls during the fight,

player.modav dragonsouls 3

I do not know if these console commands (esp. the first two) are going to cause problems later on in the game.

thank you Train & Kali, the console option is much simpler for me (though I do not know if it will cause problms in game later on)

Well, the question Trainwiz is how and where do I use this. Sorry, completely unfamiliar with the CK...

But it in your data/scripts folder, duh.

I got past this by disabling the unoffical skyrim patch, i have no clue why it was that one, but the fight went normally after then i turned the mod back on.

I'm stuck with the same problem and am quite the noob when it comes to computer files and such. How can I get this quest to end with console commands?