I have been experimenting with Anki and guitar scales, too.
First, remember that Anki alone is not a complete learning system. It is very good at what it does, but it does not do everything. Your goal is not to memorize hundreds of scales, but to be able to use scales to create music. So, after you play the scale on the card, use it to invent phrases all over the fretboard. You don’t want to just be a robot absorbing information. You want to be an artist saying something compelling.
You could also create a card for each key. This will result in you rating the cards as “easy” faster and eventually you will have the scale in each key distributed throughout your deck.
A variation on this would be to make cards that each start the scale on a different tone and in a different key. For example:
Shape: E CAGE Major
So you would be using the E CAGE shape to play an Eb major scale, starting on the third of the scale on the first string, descending. Play it in a loop from that starting point.
The benefits are that you learn the specific tone locations of each shape, rather than a route that always proceeds from lowest to highest and back.
You can also include sequences as variables. For example, “Ascending thirds”. After you practice that card, invent some phrases that incorporate ascending thirds.
I have a bad memory. I see the Anki algorithm as optimized for memorizing a single piece of information. A scale pattern for one scale has many notes. So, if I have just one card, I end up failing it a lot. That’s why I make several cards that approach the same information in different ways.
I will also write three goals for each session on a piece of paper. For example: hammer on; Robert Johnson lick; angry. So, I will try to create phases that use hammer ons, elements of a Robert Johnson, and sound angry–not necessarily all on the same lick. These are just concepts to keep me from falling into a rut. I choose them intuitively.
So those are some possible ideas. Let me know if any of them help you.
Things can get out of control if you try to create every variation for every shape in every key. So you have to be careful not to become obsessed with “completeness”. Don’t add a ton of variations on the same shape all at once. You can always add more later, when you are ready to explore new concepts. Do several variations and then move on to a new shape. You will ultimately learn to use the shapes musically by using them musically. Remember that learning any shape at the in a given position on the fretboard will help you play all shapes in that position. Everything overlaps and is interconnected.
Spend at least as much time making music as you do practicing with Anki.