My original plan was to allow the player to toggle any augmentation on any ability they had, but my concern was that there is likely an optimal augmentation for each ability, and adding the RNG would keep it more interesting by preventing the player from always being able to just go with their favorite. That's also why I only have one augmentation option per level.
I agree that the whole game could be more intuitive. I was watching Vimlark play it and in his first run he kept choosing more augmentations instead of levelling his abilities to increase his damage. It would be easy enough to pick up after a few runs, but for jam games very few people actually play for that long.
Thanks for the feedback, and I'm glad you enjoyed it!