Copy-paste from the discord chat:

When I noticed the cost per ability increases with the higher charges, I started leaving my abilities at level 2 or 3. Getting all charges of my abilities back is like, 150 scalar
or less idk, i usually only need to restock a couple charges of a couple abilities so its basically free
I feel like it should be reversed
like, if you have 2/3 charges, that one should cost 100 gp and 5 scalar, rather than the 0/3 costing that much
that way it discourages using abilities too much, but encourages using them a little (while still actually upgrading in tree)
because as it is once i upgrade its going to immediately start costing more resources to play

tl;dr- Make the most expensive ability repurchases the ones when you have used more charges, rather than making it be your 8th, 9th, etc charge regardless of how many were used.