The main thing is that mages and commanders are far less dependent on equipped items compared to the other classes, they employ their benefits naturally without the need of combining them with what they wear. Assassins, Warriors and Defenders can be as powerful or even more important in certain situations IF they find the appropriate equipment:
You find a rare/unique bow and suddenly your assassin has become a killing machine combined with the ignore defence and critical damage traits.
You find a rare/unique armor and your defender can withstand basically every kind of damage combined with his damage/spell mitigation traits.
You find a rare/unique melee weapon and your warrior will have the highest damage output on regular troops in the entire game combined with decimate and other traits.
In addition, only if you have the right equipment all the different class specializations come into play so that the assassin will be a champion killer, the warrior will be the trained troop killer and the defender will protect your army from Fear and other spell/damage effects. The problem is not the trait trees, it's your forced reliance on luck concerning what loot you find. This needs to be addressed.