Mod have you considered eliminating the antagonistic hit for taking a faction commission? The reason I ask is, if you have all factions enabled, most factions have at least five enemies, some of which are VERY powerful. In effect, taking a commission is extremely dangerous, especially early on, particularly in regards to making the templars antag you, since they are enemies with everyone I think, so de facto taking a comission with anyone is declaring war on templars (BAD)
What I would prefer is, no antag from taking a comission, but obviously it blocks you from taking other comissions, and gives you an antag hit if you give up your comission with the giver. Moroever, the comission scales with loyalty in addition with ship size, so that it pays little for killing frigates at low loyalty, but high for killing capital ships at high loyalty. The comission system becomes, in effect, an incentive to take on powerful faction enemies and also rewards long term loyalty to a faction, but does not bring down the wrath AUTOMATICALLY of every enemy.
If that balance is too far skewed, maybe make it so commissions prevent you from using enemy bases, even while stealthed