Thanks for trying it and sharing the feedback. I hear you... I'm working on a full redesign at the moment that is almost complete. In addition to making the highlights/annotations optional, it introduces a minimal "full screen" view that activates automatically when you scroll/paginate/tap blank space and makes the annotations much less prominent and hides navigation UI. I will post a screenshot of the WIP here in a moment.

I will consider more automatic ways of tracking reading progress as well. And I will make this tracking far more valuable soon too: it will automatically review your flashcards (ones that exist and ones you create in the future) when you read the words/kanji that appear in texts. This will also automatically transition words to "known" status simply by reading and applying the FSRS algorithm to it to determine learning status maturity levels based on the resulting intervals.

Yomitan is also absolutely a goal, and high priority. I'm working on Yomitan custom dictionary import at this moment. I hope to launch this very soon. Besides bringing your own dictionaries, it will also include Wiktionary ones out of the box so that you can get monolingual lookups easily (which will also let me add more languages than English for Japanese lookups).

Here is a roadmap: https://blog.manabi.io/articles/manabi-reader-roadmap/

If you have any other feedback please let me know, it's very helpful.

EDIT - some screenshots of the redesign:

The new bottom navigation, including the audio player (for which there is also synchronized text highlighting, karaoke-style): https://media.discordapp.net/attachments/1383634595697918062...

The karaoke highlighting of text synchronized to audio: https://media.discordapp.net/attachments/1209908367821373500...

Updated lookup popover navigation with sentence and paragraph tabs: https://media.discordapp.net/attachments/1383634595697918062... I am also now adding sub-word lookups to this...

The full-screen view of an ebook: https://media.discordapp.net/attachments/1209908367821373500... (I am going to minimize this further, and will also have JLPT level underlines off by default)