SumatraPDF is my most used and most beloved program.
The option “remember these settings for each document” is problematic. If you open more than 10 pdfs per day that is more than 3650 stored settings per year. It should be possible to choose the document which I want to remember and safe settings only for this one. An easy solution would be to set the option only for the current doc and then reset the option automatically.
When settings like favourites would be stored in a separate text file per document, the favourites could be extended with annotations over the standard text editor.