I would recommend looking into the Zettelkasten ("slip box") system, then ("How to take smart notes" by Sonke Ahrens is a great read).
Particularly to your point (2), the problem I've seen with most systems is they are not simple to maintain. Contrast this with "Getting Things Done", which is practically the simplest productivity system I've ever used that accurately works, where you have only two chores:
1. Write down tasks as they come up
2. Flesh them out later with as little metadata as possible (typically, at most, a project + due date if necessary)
The Zettelkasten mirrors this in a lot of ways. It has the advantage of re-writing your notes in your own words (your point (1)), but it is very simple to maintain. You re-write, make links to other notes in your existing setup, and you're done. Your notes should be as context-less as possible (which causes you to think further), and you should generally be able to relate it to GTD's daily "review" process.
A big point of clarity is the Zettelkasten is against "organization" - everything falls into the box. Ahrens talks in depth about how folders, categories, and even tags can be very limiting - you think about the metadata more than the actual content, which gives us a headache to maintain. A system should be as friction-less as possible if we want to actually use it.
Additionally, he does address your (3) to some extent, but it seems like you've figured out what these thoughts are, and resolved that they probably aren't worth fleshing out further (beyond maybe your proof-of-concept, fail-fast demo). I imagine if they are worthy ideas you probably would elaborate on them further.
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I've been using it for a while now, and I can personally attest that it's been very helpful, especially as I've progressed into more architectural/design work, and less direct day-to-day coding.