I have a very similar problem. I bought a Kindle years ago because I thought it will solve all my reading problems - I wasn't even thinking about annotating stuff, so my use-case is weaker/easier than yours.
Now, I tend to do two kinds of reading - (1) research papers - often with multicolumnar writing, tables, diagrams and mathematical notation (2) "normal" books.
I realized that kindle is very bad for (1) ---- I could load a PDF but then I don't get to use flow, and given the screen size, this can be annoying. Converters (like calibre) don't always work. Math symbols (which can show up mangled), diagrams and tables can get displaced from the "region" of discussion. Eventually I just moved to read stuff of type (2) on my Kindle. For (1), I still use printouts.
Now, I tend to do two kinds of reading - (1) research papers - often with multicolumnar writing, tables, diagrams and mathematical notation (2) "normal" books.
I realized that kindle is very bad for (1) ---- I could load a PDF but then I don't get to use flow, and given the screen size, this can be annoying. Converters (like calibre) don't always work. Math symbols (which can show up mangled), diagrams and tables can get displaced from the "region" of discussion. Eventually I just moved to read stuff of type (2) on my Kindle. For (1), I still use printouts.