'Commander' trait needs a buff
Currently, picking Commander at level 2 just gives the hero the ability to produce -15% unrest by being stationed in a city. This doesn't help the Commanders who follow the combat line at all, making Commander the most unappetizing trait in the early game. Buff Commander to give both the -15 unrest AND +1 army initiative/some other bonus so that it becomes a bit more flexible and isn't 100% useless for combat Commanders.
In general, the Commander trait tree needs work. It's also a problem that there is no good way to gain experience for Commanders who do exactly what they're supposed to be doing; commanding/administrating a city. The Commander trait itself should additionally provide a hefty experience bonus when stationed in a city so that running a pure administrative hero who never fights becomes a real option. This could serve as either an alternative or an addition to the above proposal. In addition to this, Administrator 1-3 should each provide an escalating XP bonus for Commanders stationed in a city (and please, StarDock, it needs to be a lot more than the +1 XP/season you currently have the Adventurer's Guild at; this is a ridiculously low amount of XP).
I'll also point out again that the 'Innovation' trait from the Loremaster line isn't strong enough: While an instant +100 research is strong (though I'm not sure if it's bugged, I seem to get a lot less than 100 research when unlocking it - it seems to just finish the currently researching tech?), Loremaster III provides +3 research/season, meaning it overtakes Innovation in just 34 turns. In comparison, the Merchant series has +5 gildar vs 500 instant gildar for a 100 season ratio.