So I got a nice new gaming PC and have been playing Skyrim in all its fullest glory. Replayed Dragonborn recently, and despite having played through it several times on two systems, only now has it come to questioning:

What does Hermaeus Mora accomplish at the end of Dragonborn?

He strings you along to defeat Miraak. Why? Because then Miraak rebelled against him to escape Apocrypha and return to Tamriel. The reason why this is a problem for Hermaeus Mora is questionable, though I believe it to be because Miraak only wishes to serve himself, not Hermaeus Mora. He wouldn't be a Daedric Champion, but his own. This desire could have easily been quelled by allowing Miraak to return to Tamriel the same way he left it: a powerful servant of Hermaeus Mora. But rather, he trapped him in Apocrypha and allowed him to become bitter and resentful towards his master, leading to his actions in the Fourth Era.

But then the Last Dragonborn comes along and Hermaeus Mora has him kill Miraak and take his place. Except you're no more under his control than Miraak was. In fact, even less, considering Miraak was at least fully empowered by Hermaeus Mora, whereas your power comes from your own accomplishments. And unlike Miraak, you can move freely from Tamriel to Apocrypha under your own autonomy.

So what benefit is it for Hermaeus Mora to lock up and kill his powerful servant as a trade for an even more powerful being that is completely out of his control?

Granted, I don't think the main story for Dragonborn was very well-thought to begin with, having way too much of a focus on Hermaeus Mora than, I don't know, the Dragonborn, but I'm still going to question this.

Miraak wasn't fully powered by Hermaeus Mora, Miraak was once the head of the dragon priests during the age where dragons ruled over skyrim and the Nords. He was already powerful before he offered his servitude to Herma-Mora.

Herma-Mora's intentions are unknown, that is true, but he does supply the LDB with something that drove many people insane. Infinite knowledge and the ability to change what they know, that can drive a person completely insane. Herma-Mora probably thinks he could bend the LDB's will with this power, he is also getting dragon souls from what the LDB's thirst for change, souls are like cosmic currency to the Daedric Princes and I imagine the more unique the soul the more it's worth so Herma-Mora would essentially be getting the purest and richest of gold.

While we can move freely from Nirn to Apocrypha there is nothing to state that Herma-Mora's influence isn't ingrained into our very soul, he could be turning the LDB, making him more and more hungry for knowledge and tempting the LDB to return to apocrypha. For all we know we could be on a leash that Mora is secretly controlling.

YMMV, given that everything after the quest indicates that you are not technically enthralled by Mora have the ability to go about and do your own thing. Mora even lampshades it by saying you'll either be "Miraak's successor or a worthy adversary". Really, he got a little upstart to learn his place and the secrets of the Skaal that he's been after for a very long time, so he did get something he really wanted.

^Like I said, I don't think Mora really cares at the end of the day given that he's pretty apathetic toward the whole situation. Given that everything post quest points to "Do whatever the hell you want", whether or not the player is going to be Mora's plaything is up to the individual.

Another thing is this could have all been just a game to Herma-Mora, just pure entertainment. It's probably the reason why he didn't take care or Miraak himself.

He gets the Skaal's secrets.