In my experience on WoW, I believe missions of some kind would be helpful. Especially in between raid availability. An NPC for example should direct the player towards developing a skillset, and there can be some incentive to complete the NPC task by rewarding the player with mundane but otherwise harder to obtain materials: some gold or iron nuggets, etc, for example, or depending on NPC lore some enchanted books perhaps. This would maintain a vanilla aspect as villagers already provide players with 'missions' to trade so many wheat for example. The player must farm or collect wheat in order to collect the reward. These missions however would be directed specifically towards development of the skill nodes you wish to implement.
I hope this can be a beneficial contribution. GL! I am also interested in visiting your server at some point; that does sound quite interesting, I tried something similar many years ago but dropped dev.
