Firstly I would say the doff system is really cool - and the current build on tribble is a really good start.
My suggestion is to link the earning of CXP in the various tiers to other in game things, such as the way Diplomacy currently works, so that it wasn't just the doff system that was the only means of levelling up the Tiers of CXP commendations.
Current Diplomacy Missions:
Looking at the current variety of Diplo missions (both randomly generated in Explore clusters, in patrols and available from NPCs) some of these might better be suited to awarding other forms of CXP.
Eg, ones where you are scanning medical supplies, or delivering medical aid to a planet could actually reward Medical CXP rather than Diplo.
Other ATPs not necessarily to do with improving relations might award trade CXP. Scanning data might be Science CXP.
Other Storyline/Patrol missions coud also start awarding different types of CXP, eg the Section 31 arc with Frankline Drake could award Espionage CXP.
This could earn Military CXP (participating gives a small amount, winning gives a larger amount, Challenges are exempt to prevent exploiting)
This could give Engineering CXP (possibly Science depending on what you were crating - but I think Engineering fits better)
Scanning these could also give a very small amount of Science CXP in addition to the data.
Trading items on the excahnge could give Trade CXP (this would have to be thought about considerably to prevent exploiting and I havent quite mastered how this could work in theory).
Recruiting into fleets/recruiting in game:
This could award Recruitment XP as could earning Boffs as you level up.
Develompent CXP: Captain/Boff traininer training Boff skills
These are initial suggestions, but I think there should be other methods of earning CXP other than just the doff assignments. Also I think Diplomany should be scaled to the same level as the others for consistency. (100,000 T4 and peoples currently earned points/rewards given by missions are scaled appropriately.)
I love this idea and there are of course more ways these things could be linked. Crafting --> Engineering. Scanning Carnivorous plants, entities, Poikliothermic tombs, etc could all fall under the purview of Science. Etc etc. I was really hoping and epxecting this would happen, and I'd not be surprised if it does. Why not have analogous ACTIVE actions one can take for the more passive DOFF actions.