I thought the idea was great, I think it's awesome when people manage to radically transform RPG Maker and surprise us.
So, this update seems like it could perfectly suit your needs. Basically, you'll create a common event that adds the desired value to a variable, for example CE001 - add +1 to the value of variable01 (upgrade era), and assign this common event to what will be called when a skill tree node is unlocked. You can create 3 nodes that call exactly the same common event, and each time you click on it, it would advance an era (Age of Empires style), or create different events and variables as you wish.
Let me know if you need anything, and if you encounter any difficulties, just let me know, I'm here to help!