One of the more useful guitars tools I've seen online. Well done and thanks for sharing the link!

A couple of suggestions to make it more user friendly:

2) For each of the scales you could also have the modes colour coded (possibly to appear if you click on the root note of the mode) - when I look at the key of E for example the notes in the key come up all over the fretboard.

2) Although I can play guitar I know little about theory so I don't know what an interval is... I wouldnt know how to tie in the relevance by clicking the interval button. Maybe a brief explanation of basic theory behind the buttons might make the whole thing easier to use.

3) Explaining the various scales in detail wouldnt be necessary but an add-on that would allow you to input the chords you are using to provide the names of relevant scales would finish the software off and make it one of the best resources online.