Hacker News Reader

No pun intended but the solution there is to buy an alternative tablet or device.

Agreeing with your main point: Apple does not provide a great solution for ebook library management and sync to iOS.

But there are good third-party options.

I recommend Kybook 3 on iOS for ebooks. OPDS sync from Calibre works well.

I only have occasional use for an iOS CBR/CBZ reader, but ComicFlow has worked for me, without any memorable problems.

That’s not an iPad problem, it’s an app problem. And there are tons of iOS apps that have solved that problem.