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Not as complex as the letter writer thinks, not as complex as most of these letter responses make it out to be.
Philosophy guy - yeah, you're sad he broke up with you, that you lost it before you were ready to admit you'd already lost it long ago. But - it's done, and it's more than past time. Anyone that puts that burden on you of always being perfect or else, someone you really don't get along with that well - yeah, it would never have been right.
Doctor guy - IMO - he's a decent guy, who is a bit malleable, got taken in by a bunch of Burning Man anti-realworld pretension, went with it, found out he was wrong. You need some mourning time for your old relationship - but don't turn it into what it wasn't - philosophy guy was what you settled for. Tell Doctor guy you need a little time, then see if the old spark is there, if he really has changed. He was a jerk - but he apologized.
It's just not that complex - figure out who you do and don't want to be with. It's not pretentious to want to do things, change the world, have goals and ambition - that's a good thing, that is how the world changes, how infectious diseases in the third world are cured. Nor is it all that unusual, and grad student focus, however much it may be annoying to those of us who have to live in more complex worlds, is there for a very good reason - to get you through grad school, to learn what you need to know to make a difference. Go for it.