I haven't worked with my supervisor for long (~3 months now, 4 when apps are due), and she is well known in her field. I understand she has a reputation to uphold is honest in her letters from what I hear, so she really needs to get to know you before something like this.
I will be giving a lab talk on Nov 15 and submitting a research proposal and lit review on Nov 19, but sadly apps are due earliest by Dec 1. So, again, understandably, she told me she didn't feel prepared to judge me in a span of about 10 days (between when I submit and when apps are due), and that I should seek another prof.
Luckily, I'm working on another independent project and I've asked that supervisor (fingers crossed!); my other references are from (1) a 1.5-year work supervisor from when I was a research assistant and (2) a prof I worked with for a summer independent project.
How will it reflect on my Master's applications if I don't have a reference from my thesis supervisor? Is there anywhere I can explain the situation? Or, is there a possibility to request a delay in submission anywhere - and if this is the case, should I mention it to my prof or should I not persist?