I think we should be able to research all the doctrines, but only be able to apply one to each unit (or maybe rather: HQ), so that we could have branches of speciality, if we are willing to pay for the extra research required to invest into two (or more) trees. Switching a unit´s (HQ´s) doctrine would temporarily de-org it (s units - and incur an officer-cost if those are still in). Penalties could apply if units of different doctrines are used together (in command or in battle). Officers, if still in the game, could accumulate a tad more slowly, if multiple doctrines are in use.
This would add a layer in giving two basic options, with somewhat of a continuum in between: A generalist army, or a specialed one. Do you take the heavy investment and inflexibility of having your amored corps going with ´blitzkrieg´ and your infantry armies with ´human wave´, or do you rather have an allround army on ´grand battleplan´ for all and spend a significant amount of research on something else, instead.
Balancing and AI-coding would probably become a bit harder because of this, but i think, it would add to the replay-value of the game, as you might want to try at least two games with each major, just to try both approaches concerning this for each (and many more games for other reasons, of course).
Interface-wise, it would be a matter of a button on the HQ-tab, displaying the currently chosen doctrine, naming it in the tooltip with the bonuses it applies and triggering a drop-down-menu listing the avaiable doctrines, which in turn would be tooltipped with name and stats-boosts to be applied, if chosen. As HQs have zero org when created anyways, and switching is penalized with deorging, there is no need to pick a doctrine on creation, just maybe a button to choose a default somewhere. Plus ledger integration (an overview showing which HQ runs on what doctrine). That should be it, pretty much.