I recently found this tool you made, and I have put it to good use for myself. In the short time I have used it, it has already made a big difference for me. I started with the default settings, then when I had done reasonably well with those, I added Causative. I later followed that with Passive, Desire, and て-form, in that order. (I have to admit that I stumbled over Desire a fair bit, especially Desire Polite. I also have trouble with て-form when mixed with Negative.)
Admittedly, I wasn’t able to start with it right away. I have already made a number of failed attempts to study Japanese conjugations, so I needed something to teach me what would be drilled here. Since I use an Android phone, I searched on Google Play for something of the sort, and I came up with this: Katsuyou Renshuu. It dovetails well with your web app, in that it teaches the conjugations at first, but then your app is better for actual practice, mostly because it uses combinations of forms instead of each form in isolation.
I also went back and read this entire thread before commenting, so that I would be prepared. For the Plain vs Polite issue discussed above, had you considered replacing those two checkboxes with a dropdown list (or a set of radio buttons) with the three options “Plain only”, “Polite only”, and “Both plain and polite”? That would remove the ability to select the nonsensical combination where both Plain and Polite are unchecked.
Another idea crossed my mind, though it might be out of scope for what you are trying to do. You could add small “Info” buttons next to each of the forms, which would bring up a popup box with a short summary of each form (the meaning it expresses, a few example conjugations starting from the dictionary form, and other such things; so nothing terribly fancy, at least).
Again, it’s an excellent tool, and in the past few days, it has taught me more about Japanese conjugations than I have learned in weeks or months prior. I greatly appreciate you building this!