A suggestion I made back when Mids was working on this by himself was an "enhancement bank". It would be basically a tab that opened a list of, say 20, groups of 6 slots, each with a list of enhancements already slotted by the user.
When you want to enhance a power, you click the power, then the bank tab, then the row you want. It would fill in from left to right, so if you have use four slots instead of 6, you still have a say in which four get used.