Really good observations.
With regards to English->Japanese cards, I actually decided not to support them in the app. I used to study with both J->E and E->J flashcards, but I find that E->J gets you into the habit of thinking about one-to-one relationships between words in English and Japanese, when most of the time the relationship is not that simple. I found it more effective to study only J->E, and internalize the general meaning and "feeling" of the word. Then, as you start to encounter it in natural contexts, you'll internalize the subtleties to the meaning. When you go to produce Japanese, it's best not to start from English and translate to Japanese anyway, so I found the most important thing was to internalize the Japanese words.
The whole experience you mentioned where you either didn't create flashcards for words you encountered, or stopped reading to catch up on generating flashcards is exactly why I built Clippings. And you're right, they aren't going to be perfect, but I still think it's way better than doing it manually. 手入れ is a good example, here's how that would work in Nihongo:
When you create a clipping that included 手入れ, a flashcard gets created with 手入れ on the front, and "repairs, maintenance, tending, trimming, grooming" on the back. That's the primary meaning in the dictionary. If you get to that flashcard, and that doesn't sound right, you can edit the flashcard to add to or replace that backside text with "crackdown, (police) raid". There's no way we can know which meaning was intended in the text, but we can at least make it easy to edit. And if you want, you can always add your own custom text to be displayed on the back of the flashcard. If I encounter a sentence that really clearly shows how the word is used, I'll often add that on the back in addition to the dictionary meaning.