This is an innovative approach to the theme. I really like the concept, but I'm terrible at playing it.
I understand what to do, but how to do it effectively is unclear. I did feel like I was at the mercy of RNG with the rewards; the first time through I got a soldier as an upgrade immediately, the second time I got saws, and my next offensive ability was also saws, and a soldier came along much later. The saws seemed great at first, but I couldn't aim them to save my (castle's) life. They sort of spun around the point I clicked on, so actually selecting an enemy I wanted dead didn't work very well, I had to hazard a guess to where the enemy would be when the saws would be circling to intercept it.
The idea of connecting all the runes together to make them more powerful is great, yet most of the upgrade runes are huge and can't easily fit into the board at all, much less line up their connections effectively. It led to me choosing to upgrade the castle so I could have more rows, but this comes with the trade-off of firing each individual rune less frequently, so it's hard to tell if it was actually making my overall abilities better or not. There were many times where I'd get an awkwardly shaped rune, such as a three long/one high with connectors on the top and bottom, which I couldn't possibly use.
Being able to rearrange the runes completely at any time is great, since the game pauses to allow for this. On the other hand, it does mean that every rune unlocked encourages the player to take everything apart and look for a better arrangement. I don't think that's a bad thing, simply that the methodical nature of connecting everything doesn't quite seem to mesh with the constant need to respond to enemies as the game progresses.
I'm sorry if it seems like I'm complaining a lot or nitpicking, I think this is an excellent game idea. It might be that the problems I see are more a skill issue than anything; either way I think you did a great job overall!