I used Gerty for the one class I’ve had with an eBook with great results. If I recall, for basic use, there’s a bar on the edge to remind you to buy the full version that is really easy to ignore. The rest of the features looked nice but I had no need in my use case.
I like how the new Zotero app for iOS/iPadOS doesn’t actually alter the PDF - it just saves them to a database and displays them superimposed over the PDF as if they were embedded in it. I’ve had so many of the PDFs that I heavily annotate become corrupt over time, breaking the OCR layer. The file format was never meant for note taking, it was supposed to be an intermediary digital format for proofing documents before sending them to the printer.
On macOS, the Skim app is based on this same premise. But AFAIK no other iOS app lets you visually annotate the PDF without altering the underlying document.
I use the Kindle app when I want to synchronize the reading position across a pool of devices including non-Apple ones (kindle, Onyx boox).
I also use voice dream reader as a whispersync alternative, when I want to read something faster or if I attempt to run on a treadmill.
Finally I use DEVONthink to go to search and read a database of reference ebooks I am keeping synchronized across my devices.
Regarding Marvin updates: I discovered the Mobile Read forums back when I was having sync problems with Marvin 3. One section is devoted to Marvin apps (https://www.mobileread.com/forums/forumdisplay.php?f=260). There’s a lot of noise there but some informed discussion as well. It includes threads discussing Marvin updates. They’re likely never happening, in their opinion, and there’s some forum history there about the developer moving on from the apps and those forums.
I still love this app despite the problems I’ve been having with it. I switched back to Books for a bit for my fiction reading at one point and that pointed out to me what a great reading experience Marvin 3 is when it works. It’s sad to see that it’s no longer being developed.
It is a bummer. I enjoy using Marvin as well, and wish it would be updated/maintained, even at a minimal level. I wonder if anyone can get in touch with the author and see if they would ‘open source’ the code on GitHub. Or get Automattic/WordPress to buy it and revive it!
While that may indeed have been a popular use case, that’s a misconception. PDFs were, from the very first iteration of the specification designed and intended for interactive viewing and (editable) annotations:
“The document’s text may be searched and extracted for use in other applications. In addition, an Acrobat Exchange user may modify a PDF document by creating text annotations, hypertext links, thumbnail sketches of each page, and bookmarks that directly access views of specific pages”