I think that the following 2 changes, taken from the TT, would improve the quality of the game in general (including the Campaign) and be especially useful in MP:-
1. TT based unit caps
I think that, at least in MP, unit caps based on the Core-Special-Elite classification should be implemented, where the army can only invest so much funds into a particular type of unit. This would allow for better balancing between units by limiting the supply of elites and thus allowing for elites to be balanced as an actually limited resource rather than just off their cost.
This could, at least when applied to the AI and as an optional system for the player also improve the campaign by leaps and bounds by restricting the AI's tendency to field elite spam armies and armies composed of ludicrous unit comps. This could also allow for better balancing of core units by making their numbers affect the availability of other types of units.
2. Blind Picking of factions and armies in MP
This would require that the player both pick their faction and build their army before queuing for the MP. This would have the following positive effect on the MP and balance in general:-
A. Reduce the spiral of increasingly niche and enemy faction specific armies that seems to afflict the MP. A player would be dependent on their own tools and build their armies according to what they wanted to pull off rather than to address the specific weakness of whatever faction the opponent would have picked.
B. Bring the MP and Campaign closer in terms of balance and reduce the conflicts between the 2 by making the MP conditions a little closer to the Campaign in that armies are not built just to take on one specific type of foe. This would also improve the overall balance, which is important since the two (Campaign and MP balance) are connected and thus would be better off when similar considerations prevail across them.
C. Make identifying poorly balanced units easier to spot through pick rates. The present system makes identifying such units somewhat harder, since their situation is obfuscated through their utility in niche and marginal cases (often dependent on knowing the enemy faction beforehand), which then has an effect on them being balanced accordingly, and therefore having a negative effect on their general utility and Campaign balance.