My university recommended I use a manuscript appraisal service that charges $90 an hour

Beta readers can only take you so far. They are not publishing pros and there may be a sizeable gap between what your beta reader thinks is a great novel and what a publishing pro thinks is a great novel.
But I wouldn't go to a book doctor/editor until I'd been through several beta readers and rewrites

waylander said:

Beta readers can only take you so far. They are not publishing pros and there may be a sizeable gap between what your beta reader thinks is a great novel and what a publishing pro thinks is a great novel.
But I wouldn't go to a book doctor/editor until I'd been through several beta readers and rewrites

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That's true. I think though, that if you're finding that your beta readers keep coming back with fatal flaws that need to be fixed (whether it be plot, character, dialogue, or prose) then you need to consider how much a book doctor can feasibly help you. If you really need more practice writing, then having a book doctor isn't going to necessarily be a good solution because what happens when you write the next book? You'll just have to hire one again.

In general, if a beta reader (or two) are big readers and they know your genre, they'll be able to tell when something doesn't work. IME. YMMV.

Not everyone can find a beta reader, let alone a competent one interested in the genre they are writing in. Yes, getting unpaid help to scrutinise your work before paying for help is more economical - but not always feasible for everyone.
I just think that paying for competent editorial services works for some people and can be a valuable learning experience. Quite a few editing services will offer to do just a couple of chapters rather than a full manuscript. You can then apply the lessons learnt on those two chapters to the rest of the manuscript.

I will point out that even people as far up the ladder as George Lucas never really learned from their previous beta-readers and co-writers. It's just that at George's level, not enough people were able to dissuade him in time from the whole Phantom Menace thing.