Although he's using the word controlling, I don't think he means 'control' . I get the feeling that what he means is that he hasn't acted on his opinions & values, and has gone along with yours by default.
But does he know what his own values and opinions are? I very much doubt it. It sounds to me as if he has never spent any time self reflecting, he's just gone along with whatever happens in his life without giving it any thought.
You suggested living together, marriage, children. You suggested moving out when you have problems in your marriage. You then move back in again. You suggested flat-sharing. He's never proposed an alternative. He never disagreed. He has handed you the reins of his life, which you have been steering, alongside your own life. You're not controlling him, you are going your own way and he is being taken with you. (I say this assuming that he didn't ever disagree - if he did and was silenced or ignored, then that is a very different dynamic).
But, it's not just you who steers him. His mum suggests he talk to you about her problem with your mum. He could have said no, had his own opinion, decided on his own what to do. He even met with a friend before talking to you last week - what's the betting the friend suggested what he say to you, too?
Does he actually know who he is? What he wants? Does he like himself? What does happiness look like for him? (It's easy to say "I'm not happy", but the important thing is understanding what will make you happy, and why).
These are not your questions to answer. He has to spend the time discovering these things out for himself. He may never do so.