So I really like the idea of doctrines not just "buffing" a unit, but actually changing its functionality. I feel that some of the current problems with spam and doctrine stacking exist because too many doctrines straight up amp their respective units.
When I say changing the functionality, I mean that it actually alters the role, and thus your playstyle with that unit. In this way, doctrines could provide both substantial buffs AND drawbacks.
For example, the dire avenger doctrine that buffs their shield is boring, and a straight buff.
Imagine instead, it buffed their shield, and removed the weapon cooldown, but also lowered their weapon range, changing them from a hit and run unit into a brawler.
Or a doctrine could be added for the big trakk that removes the "kill em far" ability, but also substantially increases their damage, and buffs their health.
I feel that doctrines that have big benefits AND drawbacks would allow doctrines to much better suit the players "playstyle"