Well, I sort of did that already, but I can try to be a little more clear. It will likely require my Learn Skills By Use script, but it will be setup along the lines of your third option. Essentially what I plan to do for each skill that has levels is, upon startup, separate each level of it into a new skill (this script will need to be below your melody scripts, by the way). There is some trickiness, in that I may need to redefine the $data_skills global variable a little bit, but there's no reason for you to worry about that since if I do, I will do it in a way that shouldn't impact any other scripts.
Anyway, the notes will be set up in a similar manner to your third option so as to use bbcode-esque tags like this:
\level[X] /level[X]\level[Y] /level[Y]
Notes within those tags will apply only to that level of skill, while notes not within any level tags will be included in all levels of the skill. I will also include codes for changing the values of regular options like damage and variance, but I haven't settled on exact format yet. Naturally, I will include tags for you to set level growth as well as options to explicitly set how many uses are needed for each level.
Anyway, you don't need to worry about these things. If I find I am unable to do it, I will inform you. Until then, you can assume that I will work on it when I find the time. I still need to do a few other scripting tasks before I can start on this, but they are fairly minor. As I said last Sunday, you can at least expect that the script won't be done before this Sunday.