Some time ago, I settled on a combination of Calibre and MapleRead for my eBook storage and reading solution.
I travel a lot, and did not want the prospect of a book I was preparing to read magically disappearing. That is not how things should work. With the combo I currently have, I am in full control of my eBooks, and I decide what gets onto the iPad and where it is stored.
It might not be the user-friendliest solution - Calibre does require some work to get used to, but it is brilliant, and I have tried all the major eBook reader apps and settled on MapleRead because it does what I need, has powerful search functions and just works.
I too was initially a user of Apple Books until I got fed up with it randomly offloading stuff. I also used Marvin (which I happily paid for) for a couple of years, but that is abandoned now; MapleRead however, reads all sorts of formats, which is another reason I settled on it.
I, too, love Calibre—as a library maintenance and metadata tool—but found using it as a server, at the time with Marvin, was too complex and required too much time-consuming customization and bug-fixing. I did try MapleRead at one point, but only very briefly—the lack of a MacOS app was a problem for me (although an M1/M2 Mac might solve that?).
As a broader point, it's odd that Apple's Books app sucks so much.
I have beta iPadOS 16.1 (20B79), and while there are some great things in it—ability to change line spacing, paper types, etc.—there are way too many shortcomings: no ability to set margins, two taps now required to access TOC, etc.
Worst of all: I often read my ebooks with the iPad in upside-down portrait mode, both because this allows my case to be propped up at the optimal angle, and so that I can charge the iPad while reading. But the last beta, for no discernible reason, took away my ability to do so! Hope this will be ironed out in today's release.
Maybe someone else knows why Apple doesn't invest more in its Books app—it would seem like even a relatively small investment would help them—not just to avoid embarrassment, but with any luck to sell more from their store.
Anyhow, thanks for the MapleRead suggestion—maybe I'll try it again. The versioning is a little complicated—if I download CX (the only free version), will it at least give me a good sense of how the app looks/works?