Sorry if those has been suggested and commented on before. I did some searches, but didn't find anything similar.
Regarding the usage of kanji in all words, when kanji has been marked as known, I'd love to see a feature to turn off their usage in words that have become commonly written in hiragana. I guess prime examples would be この, その, etc, but also things like ますます. I'm not sure whether any of the free resources used to populate the dictionaries contain that information though...
One other thing is the matching of readings with kanji... for example, although I can search directly for 固い in the dictionary, entering just かたい there or when adding to a list, doesn't return this form at all. I guess it's because it falls under the definitions for 硬い, but the nuances get lost that way. I actually stumbled upon this when one of the vocabulary study lists for Tobira made うまい (referring in the textbook to some Hokkaido potatoes) into 上手い. I'm not sure whether the word for delicious would be usually written in hiragana (as it was in the textbook), or 美味い (not in the dictionary) or some others are still in common use... but 上手い it wasn't.
I hear ya! Usually when I come upon these, I just do an error report to Michael and he takes care of it on his end. I don't know if that's how he wants it done but you're right, there are a decent amount of instances where just the hiragana should be used.
Sending an in-quiz error report is a good way to report these; just leave something in the message referring to what you think should be changed. Most 'commonly written in hiragana' terms are shown as such, but I have no doubt that there's some still floating around.