I'm in the situation that I'm completing my master's research degree and I'm in the process of applying to several applied mathematics / computational science programs.
Here's me complaining: I do research for a collaboration and most of my research work has been for the calibration field of the experiment. My relationship with my supervisor has been less than good. He originally lied about the kind of research I'd be doing and because I'm in a program where you pick you supervisor before entering into the program, my impressions of him where very preliminary and not reflective of his concern in students' interests. My current impression of him is that he's a career administrative academic, his involvement in the collaboration is merely to appear involved in research despite not being in charge or overseeing any research that comes out of the collaboration itself. In the past, I've voiced my concerns with him about needing to be more clear and direct about the work he wants from me for the collaboration, only for him to be incommunicado for several months, that is until someone in the collaboration needs something he promised he'd get for them. At that point, he comes to me telling me to get something to him in the next week, saying I haven't been doing anything meaningful; over working me. The research I do do often does involve different people from different institutions, but it's never enough to be a reference for me as my involvement with other collaborations is somewhat scattered End of complaining.
I can't switch advisors because for one, he's the assistant chair and would and would have impact on if I should be kept in the program if I request a change. And if I did end up switching, the department would likely delay my defense, which I cannot afford. I'm stuck with my advisor and project till my thesis. Which I can deal with, it's the lack of reference in my applications that worries me. Now, I have quite a bit of research as an undergraduate where I'm getting letters of reference (all research experience). But will the lack of a letter from my thesis research screw me over?