I haven't played the Dragonborn DLC up to the fight with Miraak as of yet. I've mostly done side quests (trying to hit level 65 before I fight him as I read on UESP you get the best version of Miraak's gear at that level - she's still at 64, damn beast blood slowing her leveling! not to mention I've been stockpiling dragon souls and learning new spells like nobodies business; so basically I've been prepping) and so on my main character anyway, her only interaction with him thus far has been through his disciples that attacked her and hearing his voice in her head after trying to take a nap at the Retching Netch and waking up at the Earth Stone.
I have however seen a few modded LPs and read all the lore so I think I personally can give an opinion of sorts on this, though obviously I can't yet speak for my characters. Hope that makes sense. Anyway..
Considering the time he was alive - during the time the Dragon Cult was at its zenith - I do actually sympathize with him a little. Any Dragonborn would chafe under rulers like that. Hell, mortals did, I imagine it would only be worse for a Dragonborn. So I mean I understand that he would want out of under the dragons and their Cult, and that he felt that what he did was the only way to accomplish his goal. However I don't agree with how he did it. I don't agree with the mass murder of dragons as seen by his temple or making them into grotesque decorations as seen there. That seemed a bit superfluous even considering his circumstances. I also don't like that he refused to kill Alduin because he thought it was beneath him. I dislike that he left it to the Tongues and later, the Last Dragonborn. I think he should've gone about getting out of under the Dragon Cult like the other Nords did. Team up with Paarthurnax and the Tongues and take out the "god" himself, Alduin. But Miraak didn't do this. He chose to be selfish and make a cult identical to the last all his own.
What I'm trying to say is, I have mixed feelings. On one hand I sympathize with his situation. On the other considering the way he chose to deal with said situation, makes me really not sympathize with him at all.
I do sympathize with his want of getting out of Apocrypha. However he wouldn'tve even gotten stuck in Apocrypha if he had chosen to handle things differently than he did. So again, I feel kinda like he signed himself up for that in a way and that the citizens of Solstheim shouldn't have to pay for his mistakes, or wrong choices, so to speak.
All in all, I think if I had had a chance to team up with him as he is now, I wouldn't do it. If there was some option to team up with him, help him get out of Apocrypha and help him see the error of his ways and try to change, I would pick that option in a heartbeat. So I guess my answer is: it depends.
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