You're missing "getting to work on what you decide to work on, not what someone else tells you to work on." That's the ideal, anyway--funding constraints, supervisors, colleges and units shaping what is fundable, all of these things are reality at Universities. Fundamentally, however, a Ph.D. CAN be a stepping stone towards tenured faculty, and as tenured faculty you get to decide (if you can get it funded at the level you need) what you do research on. That's huge for some people, getting paid to look into something that fascinates them.
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Your other points still hold, of course.
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