To me, the trainer seems more like a test. I liken it to a kid learning math facts, like times tables. The fretboard trainer is like a set of flash cards for all of the times tables - you wouldn't use them to learn but to practice for a test.

Follwing the anaology, you don't learn all of the times tables all at once, you learn the 2's, 3's, 4's, etc indivudually. At the end, you'll use flash card from every number and mix it up. As you are building up your math fact repartiore, you'll mix up what you've learned.

I think a logical breakdown for this would be allowing the user to specify a fret range to select notes from, 0 being the open strings. Perhaps you are comfortable with all of the notes up to the 5th fret, you could specify a fret range from 6 to 12. If you are just starting out, you can start with specifying a single fret.

You could even allow the user to specify a string range on top of that to make it really flexable. For some reason, I don't know the notes on the 2nd and 3rd strings as well as the others. With this functionality, I could narrow down the trainer to focus on what I need to work on.