I wonder how he ran it.

He was a prisoner himself, at one point.

I didnt read much of it but it seemed he did okay.

The thing that struck me was he left the New Avengers because he believed there was a better way to make change, and went on to run the prison (i think it was the raft).

Then, captain america becomes the head of shield and says "luke, i want you to run the new avengers because there should always be a new avengers team doing what the main avengers team cant, and you're the best one to do that"

And he's like "alright, sure" and just leaves his role running the prison to go run the same team he was running before

Im actually pretty sure he was done being a super hero because his family had been targeted in dark reign and he didnt want to keep them exposed to that.

But the second steve asks he seemed to drop everything and go back to basics

He had to listen, because it's captain America.

Still though, one of those things where a characters progress is just undone without any consideration.

And his wife is Jessica Jones. What's the worst that could happen?

Yes, it was a bad idea. But the reasoning marvel gave, works.

Well, his baby got abducted, he was nearly manipuled at the risk of persecution of his entire family, then a ton of other bad shit that took the entire new avengers to resolve.

The reasoning was just "because cap asked".

They could have picked anyone else to run the team

They could have.