I am currently applying for a PhD in a very competitive top tier university, which requires three references. I have two referees (my tutor and my undergraduate research project supervisor) who I am quite sure would write very good references for me.
I am stuck with the choice of my third referee:
I am currently doing a masters, but my masters supervisor is overly precise and temperamental. Although he is the "ideal" choice as my referee as he can comment on my research capabilities and working in a laboratory environment, I am certain that his reference will be lukewarm or may even be negative as I am currently having difficulty getting along with him. (ADDITION: I had only worked with this supervisor for 2-3 months. I also had an undergraduate research project supervisor who can also comment on my research abilities).
Alternatively, I have asked one of my lecturers (who I get along with very well) in my undergraduate, and he is very happy and eager to write a reference for me. I am quite sure that he will write a positive reference in support of my application. But he is unable to comment on my research abilities (just my academic capability and personality). Additionally, wouldn't the admissions tutors suspect that something is going on if all my referees are undergraduate even when I am taking a master's course??
What should I do?
PS. The problem is that he initially offered me a PhD position despite the fact that I wanted to pursue and applied for a masters programme. I turned it down as I was not interested in the PhD project and when I told him about my applications to other, top tier universities, his attitude towards me has changed and became very impatient, frustrated and uninterested. This is the reason why I am quite certain he will not be writing a positive reference for me.