As for the best system to write them all down, I chose a numeric system because when I decided to catalog all of the scales I wanted to make sure I didn't miss any.
I do have a list I could send you of all 462 heptatonic (7 note) scales, but when I was preparing them for readability, I sorted them into modal groups.
Because of the nature of the sort I used, the least useful scales showed up first. So for my own use I reversed the order. Essentially, in general the more homogenized scales are the ones other musicians have decided to use. William Zeigler used to have a site called www.allthescales.com
but it has fallen out of use (domain available).
Now, I have also cataloged all the pentatonics but I haven't managed the research necessary to provide names for all of them. I only have so much owl time to spend. There are 330 of them - not coincidentally the same number of 5 note chords - I have a sort of these as well.
I am not sure a naming system based on subjective feelings will be useful in the long term, but then I don't have a better option to give you, and calling some scale "Type 361" doesn't seem all that much better.
Similarly, one of my projects was to make a list of every possible alternate tuning for the 6 string guitar. This is available in the Elderly Instruments catalog as a disk with what I believe to be the biggest pdf document available in fine print at 21,456 pages long. I think no one will ever print out the monster. I chose alphabetical order for that.
Send me your email and I will send you a small pdf with all 462 scales. I added the book names I found for the 14 main groups and added arbitrary names for all the rest. If you want to rename them, go ahead: I can't claim to own them all, and I'd feel like a fool trying. If you're sufficiently computer literate I could send you a write up of how I generated them all, but I would relegate that to alternatives to sleeping pills.
The breaking of strings is the beginning of wisdom...