TLDR: when I read I try to read actively, which for me mainly involves using various tools to annotate content: highlight and leave notes as I read. I've programmed data providers that parse them and provide nice interface to interact with this data from other tools. My automated scripts use them to render these annotations in human readable and searchable plaintext and generate TODOs/spaced repetition items. In this post I'm gonna elaborate on all of that and give some motivation, review of these tools (mainly with the focus on open source thus extendable software) and my vision on how they could work in an ideal world. I won't try to convince you that my method of reading and interacting with information is superior for you: it doesn't have to be, and there are people out there more eloquent than me who do that. I assume you want this too and wondering about the practical details.

won't really write much about it for one reason which is a big deal: while you can highlight text, you can't leave notes. Nearest functionality is 'recommending' a highlight while reading a comment, but that's only displayed on your 'timeline'. Pocket API doesn't support exporting highlights too, or to be precise it seems to be hidden. If you need it you can use my script where I hacked around it

Mind that free version of Instapaper has got 5 notes per month limit. Personally I'm happy to pay 3$ per month for premium version of such a decent product though in absence of good alternatives. Instapaper got Json API, through which you can access your saved articles, comments and highlights. I'm using a fork of python wrapper to access it. Highlights are only stored as text though (as opposed to CSS/xpath locators), so there is no easy way to match them against original text apart from some sort of fuzzy search.