My supervisor is too involved, what should I do? Most PhD students I know have the problem that their supervisor is not involved enough. I have a different problem, my supervisor is too involved.

He wants to be a co author on all three of my PhD papers, and to get them published. 

I know that this sounds great, but I do not want to free ride on my supervisors work, I want it to be my own, and I want to be proud of it. Regardless of whether it is published or not. A publication is a bonus, not the end game for me.

I spent half my phd working on what I intended to be my job market paper (the paper I show to employers that best showcases my skills). My supervisor made some suggestions here and there, but nothing substantial. I am now getting ready to submit my paper to a journal and my supervisor has rewritten my entire paper without permission and wants me to sign off on this. He has justified it by saying it has a better shot of being published in its new form. I feel very uncomfortable about this, it is in effect no longer my paper. I thought he would make suggestions and I would fix the paper myself.

He is too involved in other ways too. When I settle on a research question, he throws methodology and research design at me, before I have a chance to think about the topic myself and come to my own conclusions, and then encourages me to do it his way and not explore my way.

Is this normal behaviour from a supervisor?
I have to talk to him about this, but I am unsure how to bring it up and what to say. Do you have any advice?

I need at least one paper where I am the sole author, is it appropriate to mention this to my supervisor, without offending him or his position? He will try to put his name on all my papers.

I do not want to come across ungrateful, I am very happy for his help, and I will be the first to admit that I need help. But all I want is a chance to learn from my mistakes and be given opportunities to grow, I will never be a successful researcher if I cannot exercise this. Unfortunately, I feel like my supervisors research assistant instead of a PhD student.

I am really struggling to continue on the course, and I appreciate any comments you may have.
The first part (rewriting your text) is quite frequent. Believe it or not, most PhD students are terrible writers and though a good adviser would patiently go over the paper with a student pointing out the presentation flaws and asking the student to fix them himself (take my word for it, you do not want to get that list from the reviewer after the paper has been submitted), I know many people who lost their patience in that respect eons ago and other people who give up after 6 months of modifications and still do the job themselves.

So, the first question to ask is "How well was your paper written in the first place?". If not too well, there is a chance that you should be merely grateful for the revision and stop at there.

The second point is "throwing his ideas at you". Here the question is "How fast are you coming with workable ideas of your own?" Giving a PhD student the solution together with the problem is a terrible idea, insisting that the student do things your way and your way only is even more terrible, but giving him no suggestions after 6 months of no progress is also not good.  

The third question is whether the supervisor should be a co-author. Unfortunately, your post is somewhat self-contradictory on this point: compare


  My supervisor made some suggestions here and there, but nothing substantial.


with 


  he throws methodology and research design at me, before I have a chance to think about the topic myself and come to my own conclusions, and then encourages me to do it his way and not explore my way.


So was that particular paper done his way or your way? In the first case, IMHO, it is his choice whether he should become a co-author or not though you may still drop a hint that "the job market is tough and having a single author paper is a nearly must to land at the place you want to go to", in the second case it should be yours even if he rewrote the whole thing and you have all moral rights to insist on a single authorship if it is important to you. How exactly to do it without offending him I don't know (different people need different approaches), but judging from the tone of your post, you have had arguments with your adviser before, so you should know better than I what upsets him and what makes him cooperative. 

So, alas, the only things I can tell you are the usual "Look into the mirror and try to figure out what exactly you see there before making final judgements" and "Hold your ground but use your common sense and pay attention to the reaction to your words when insisting on something". I should confess that I often fail on both accounts myself, but I'm in a different position than you. Let's see if other people can come up with some better advice :-).