A lot of the stupidity comes from The Data/Match/AI.xml file and the Combination of the Skills_Listing AI_iWeight , and yes if you want to make the teams more challenging you need to figure this out.
I think there's hardcoded stuff that is responsible for most of the stupidity, like you said the files we can't see/don't have access to. There is definitely an invisible layer we can't touch or see.
AI_iWeight is a dead end from what I can see; if you filter it, the list goes from 10-100 (except for stat increases and skills you can't choose like Decay). The skills range from less desirable skills (like diving catch, diving tackle) to more desirable skills like Block, Extra Arms and Dodge (which subsequently are 100%). If you look at Player_Type_Skill_Progression many of the skills under 50 in iWeight are near the end (and don't get picked much or at all if you watch closely in a campaign). It's not true in all cases though, but a good way to tell is to look at the skill kick and where it's listed in each progression table. The skills look fine with the iWeight more or less decent for each.
ai.xml however looks promising, I've pretty much ignored it to this point. Hopefully I can reduce the dodging somewhat.
Are you sure about CoolViolent? You said a lower value means they're less likely to block? Why are Chaos so low then? And Woodelves are default 0.9 and 0.9 for PassRun? Do the values go a lot higher then 0.9 or is that the limit?