I have also been at it for a while now. What I notice nowadays is that the same English->Japanese cards keep coming up quite often, because they have very similar cards/synonyms. Therefore, when adding new words, I take extra precaution to come up with a short 2-4 word sentence that is unique enough and captures the meaning quite well. Sometimes it might take me a few tries though, when I end up confusing it with another card anyway. This may also mean that sometimes I have to go and change a card/note I made a few years ago, because it 'conflicts' with something I want to add now.
So with regard to the clippings feature I feel that generating single-word flash cards might come back to bite you. It makes English->Japanese "production" difficult and annoying in the long run. On the other hand, it also makes Japanese->English unnecessarily complicated with all the meanings associated with a single word. A relatively simple example that comes to mind is 手入れ, of which I would rather have two short sentences describing each use case. Or with regards to the clippings feature, I want it to generate the card with the meaning I encountered, because the other meanings of that word might never actually be used by the Japanese.
I am not sure an app will (or even should) be able to generate such cards. Condensing both the Japanese, while getting the English meaning right, is hard enough for a human. It certainly would be awesome, because at the moment I have to resort to generating the cards manually for the words/sentences I encounter while reading manga or books on my Kobo e-reader. History shows that (1) I am too lazy to generate a card for a word that I had to look up, and that I tend to just keep on reading (and forgetting the word again later on), or (2) that I actually stop reading for a few days/weeks because I feel I have to enter the back log of cards in Anki before continuing.