Of course you can modify some files to change traits, etc. But in my mind, creating good governors or generals isn't unpleasant micromanagement, but rather a fun part of the game. If you don't want certain traits, you can learn how to manage the character to avoid them, and to do the right things to get good traits.
Some of the factors for giving negative points to traits make perfect sense to me. If you leave a general sitting around in some stinkhole backwater province with a tavern, it shouldn't surprise you to see him take up drinking. If you build temples that increase trade and leave governors there, they become greedy moneymongering cheapskates. Again, that isn't surprising.
I think the negative trait issue is very similar to the squalor issue: it is beyond many players to understand the way it works or to really enjoy solving the problem through gameplay. I was always able to deal with squalor without revolts before the 1.2 patch dumbed it down so people wouldn't complain. The same holds true for negative traits. It isn't very challenging to have positive traits develop by default for characters left to rot in a settlement, now, is it?
Managing generals is easy. Just send them to the field and give them experience. If you choose to let them develop some retinue first, then place them in a town with an educational institution and temples of law, but never temples of fun, love, war, trade, fertility, because they almost always cause problems. Temples of healing are a crapshoot for good or bad traits, but you can't go wrong with law.
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