The software that reads the ebooks must have notetaking integrated into it - a separate app won't help.
The Kindle has a way to make notes, highlight things, etc. Don't know about any other ereaders. I also don't know about the Kindle Android app, because I don't use Android. The ability to easily access a file of the notes, etc. (called "My Clippings.txt") is only on the Kindle itself, not the apps, although you can sync to Amazon (Amazon-purchased books only), and access via the web.
Rain is bad for any electronic device. Put the ereader in a bag or something, to keep it out of the rain.
PDF reading is possible on the Kindle, but not optimal, because most PDFs are set up for a large page size, so you have to scroll and zoom, etc.
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