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Hi - I can only address a little bit of your post, as I don't use highlights/annotations and there is no send-to-kobo via email that matches the Kindle feature. However sideloading works perfectly (and content loading can be done via Dropbox, Calibre content server, etc and not just via sideloading), so it's not like there's no other way to get a variety of documents on to your device.
However I can tell you that the Instapaper type features are done via Pocket on the Kobo, so perhaps you could check that out while waiting for others to address the hacks-and-workarounds side of things: getpocket.com
I also suggest checking out the Kobo Developer's Corner subforum here at mobileread.
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