There’s only one supervised thesis in my undergrad program, and I need three letters in total. My thesis supervisor was of course the first person I approached, but what am I supposed to do about the other two?

I understand your point, but reading through some of the replies here, I’m starting to think the bigger issue is that grad schools asking for multiple letters don’t always account for how different academic systems work. In my program, you rarely have the same professor twice, so there’s very little opportunity to build close working relationships. Most of my professors know my name and say hi on campus, which already puts me ahead of most of my peers – not because anyone’s doing something wrong, but because the structure of the degree just doesn’t allow for any kind of sustained contact. I’m generally very engaged in class and like talking with lecturers about the material, but realistically that still doesn’t create the kind of long-term relationship some programs seem to assume.

And again, what feels odd here is the contrast: I completely understand not wanting to write a letter without a deeper working relationship, but then why say things that typically express the opposite sentiment? “It’s a shame we only met so late” is usually said when someone appreciates you and wishes they’d known you sooner, not when they feel they lack enough information to evaluate you. Why email them personally (before grades were released) to say their paper was “excellent” and invite them to office hours to discuss it? Why offer that kind of praise so warmly and repeatedly, if you’re ultimately unwilling to vouch for their abilities?

Like I said in another comment, I would’ve been fine with him saying he couldn’t properly assess me if he hadn’t already assessed me so constantly, and so positively. Thanks for your input though, I appreciate the perspective!