They still gain experience, it's +2XP a turn. I have a general with 57/60 experience as a level 3 character, but will in 2 turns time level to 4.
Edit; I've been thinking of some ideas for your Agents, if you were to include it;
There are three types of each different agent; an Army Administrator, A Region Administrator, and an Action Skill user, each with two "trees" which determine what they're good at, with each tree having three tiers.
For example,
Champion (no longer increases XP of troops without relevant skills, nor do they add their stat to the general until the reach that skill)
-- Army Administrator Tree 1 (Improves General)
---- Tier 1; Unlocks higher levels, no real bonus apart from cheaper actions
---- Tier 2; Skill 1 (Reduces cost of units recruited, etc), Skill 2 (speeds up use of abilities), Skill 3 (massively improves general's bodyguard into combat monsters)
---- Tier 3; Skill 1 (Adds Zeal to the general, +2, +4, +6), Skill 2 (Improves Fortress Stance; Defensive and ammunition bonus, reinforcement range, enemy morale malus, how much movement rate it takes to assume stance etc)
-- Army Administrator Tree 2 (Improves Troops)
---- Tier 1; Unlocks higher levels, no real bonus apart from cheaper actions
---- Tier 2; Skill 1 (Improves troops XP, decreases movement range and increases upkeep cost, higher levels increase XP gain, but at a slower rate (say level 1 = +20, level 2 = +30, level 3 = +35 XP), but reduce the malus), etc, Skill 2 (Improves troops melee stats), Skill 3 (Improves troops range stats)
---- Tier 3; Skill 1 (Improves faction focus, i.e Roman Heavy Infantry, Spears for Greek, Horse Cavalry for Hordes etc)...
-- Region Administrator Tree 1 (Improves Friendly Region)
---- Tier 1; Unlock
-- Region Administrator Tree 2 (Malus on enemy Regions)
-- Action Skill User 1 (People)
-- Action Skill User 2 (Settlements)
Brief ideas.
Main changes;
Spies poisoning merely slows enemies until they reach high level when it actually causes damage (Tier 3 skill, perhaps with 3 levels in that skill). Abilities rely on improving movement and sight range for general, ambushing/night fighting abilities, and Improves Raiding Stance (how much you are able to forage decreasing the upkeep, how far you are able to travel doing so
Governers don't reduce upkeep cost until they choose the correct line of traits. Abilities are similar to generals administrator and rightful sovereign line - such as improving food, ammunition stores of settlements, research rates etc, and improves forced march stance (removing penalties and increasing distance etc)
Most bonuses only apply as well only when in agent stance or within army. For example, a city admin champion will only have his abilities affect the city while in his stance. If he's part of an army, it won't affect the city as he's too busy training.
I hope this helps come up with some ideas.