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The big distinction is, as Freethinker points out, between orthodox and heterodox schools. The vast majority of schools, including all or almost all of the top twenty schools teach economics in the same way, for the most part. These are the orthodox schools. To Freethinker's list of heterodox schools I would add GMU - they're extremely heterodox in their professors and teaching.
My professors advised me that I should apply only to orthodox schools. This isn't because the heterodox schools aren't good, or even that they aren't right in some things where the orthodox places are wrong. It's just that, after graduation, you'll be "marked" as a heterodox person, and that will greatly limit your options, at least in academia. Instead, they suggested, go to an orthodox school, and if you find yourself in sympathy with the heterodox opinions, you can go teach and do research at those schools.
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