I also Have thousands waiting to be Used !

The developers are working on this. 

I have read where they will soon address this I will ask about what the projected timeline on that is.

Christine Hare said:

Hi there Lord Inigo Montoya, I saw  while ago a suggestion from plarium that they might introduce upgrades in the dragonstone for Stoneheart units as many of us do have hundreds of thousands of dragonpoints just sitting there and i will Pass this onto our CM for you as its within the rules

Increasing Stoneheart Abilities could be a complete disaster and increase game imbalance

The gargoyle ability to reduce defense bonuses is a perfect example of this

My suggestion should not, but we must wait and see

Hello :)

Devs are working on the feature that will allow players to use the Dragon points they have.