When I did my big project I was using the cheap standard edition of Finereader on (virtualized) Windows, and I built an automated pipeline for it with a combination of AutoHotkey, pdftk, Multivalent pdf tools, and Python.

I too tried the Acrobat OCR first and found it to be vastly inferior. One surprise was that (at the time at least) the OCR-by-Acrobat files were not only much less accurate in the text layer, but the file size also bloated up surprisingly.