4th year PhD, considering leaving for different program I'm a 4th year PhD student at a top school in Canada studying chemical physics. For the past few years, I have been floating around the idea of leaving with a Masters and pursuing a PhD at a different institute due to many factors, such as:


Poor supervision. My supervisor is primarily overseas, and provides little to no direction or motivation in work. When discussing with him, his focus is on himself and offers little advice in regards to research.
The city I live in is not enjoyable and I find it hard to enjoy being here.
The group, while great, is not very cohesive; no group meetings, no reports, no discussion of progress at all.


For the past 2 years, I have been working on a very complicated instrument. I've spent a lot of time fixing it, as many aspects of it have needed to be repaired or upgraded, but unfortunately, finding a sample to study is highly non-trivial and has been proven to be very difficult. As a result, I find that I'm quite burned out. I have also been diagnosed with depression and anxiety (but have been treating it with medication and therapy). I've been unable to publish (but I have one first author in review after revisions, one co-author in preparation) Unfortunately, I've come to the conclusion that, due to the lack of direction of care from my supervisor's end in regards to helping myself (and other students) focus on to a project that has a clear set of steps or even overall direction, that I should probably leave with a Masters, and apply for a PhD at a different school with a project that I find myself passionate about.

The dilemma I have is that my supervisor has quite the ego. I'm certain he won't be happy with me proposing to leave with a Masters to go pursue work elsewhere. I'm not sure how to handle that; I can ask other faculty of whom I'm well-acquainted with for a reference, but I feel that the new school I apply to may question why that is the case. Maybe it's the burn out speaking on my behalf, but I am no longer passionate about what I do, and the day to day grind of improving things, trying to find a sample, and repeating is getting to me. I see other students with somewhat cohesive research goals and I look back on my own and realize there is no direction and that, I think, scares me more than anything. I don't want to run the risk of not being able to graduate. Of course, the onus is on me to be able to procure my own project or motivation, but alas, I think due to poor supervision and general lack of interest, it is in my best interest to move on to something more along my skillset and passion.

My question is, has anybody dealt with a similar dilemma? Were you able to be accepted at a different school, even if your supervisor responded poorly? Is 4 years for a Masters a waste of time or a bad idea, and should I just tough it out and finish, even if I hate it all?
My dilemma was broadly similar: I was doing a PhD in a top-tier university I hated; my advisor was awful; and I was considering leaving for a different program. What stopped me from actually doing the latter was that even with explicit invitations and introductions from helpful professors who liked me, I didn't get anything more useful than a desultory suggestion to find the department's webpage and send an application there to start again as a first-year grad student. I was three rather than four years in at that point, but I thought that was enough time that I didn't want to restart from scratch. 

In retrospect, that was a bad decision. In my case, I finished the PhD program but didn't get the contacts or publications that I needed to get an actual academic career out of it, so the five years I wound up spending at the university were a waste of time. Grad school can be miserable, advisors can be worse than worthless, and the academic market is terrible. It's just about the only way of getting the opportunity to do certain things, though, most notably serious research. If you're trying to just tough it out and finish, that may not actually get you what you want.