In Games like Supreme Commander you can easyly set wich units you want inthe game and wich you don´t. I´m not sure if Dragon Commander should have that option, but it couldn´t hurt.
I also don´t see the problem of havin like 50 research points in the skirmish set up so that you can customise your dragon. You want all the passive skills you can get? Ok. Want just to get 2 Master Skills and few small ones? Ok, I don´t see a problem.
Or at least we could have more dragons options with the preset skills.
In that matter, I also think that more agressive dragons, like the Mountain dragon, have the advantage. Why? Exactly because you can just turn into dragon, spam your Pillar of fire, and the Eye of the Patriarch, return to RTS mode staying out of harm´s way. Wait the cooldown and repeat!
And when you are in RTS mode, you can then concentrate on using your shamans/warlocks/zeppelin abilities...
So, custom dragons sounds like a great idea to me.
