The saws are actually one of the strongest abilities later on, but have a higher skill-check to them.
The trade-off with the castle upgrade was intentional, as I didn't want players to keep choosing the castle early for more room.
As for the Rune sizes, there's no real weighting system other than a slight percentage chance for how many connections there are.
And speaking of the connections, it is possible to trigger an Ability, swap a Rune to another Ability before the Ticker reaches it, and get that benefit. Though that's also a bit of a skill check with planning.
As far as balancing goes, it could use some work, but there's some higher level play and strategies I accidentally discovered while testing it that allowed some of the balancing to be less needed. Which was somewhat beneficial since I didn't have time to balance it as well as I wanted to.