Ok, here's my thoughts.

I'll work out the initial financial craziness and find out how this is actually going to work out by playing a few turns in on my own game.

On guild houses, I think the choice of the guild type that should be allowed to be constructed should be left up to the duke, so they should outline prior to their settlement reaching minor city status what guilds would be acceptable to them. But the cost for guild houses specifically should come from the Imperial coffers, and payed back later by the duke in increments, because there's no real telling when the preferred guild house will pop up, and if the duke can't pay for it right then and there he's screwed for who knows how long on the guild house he wanted.

Two other things I noticed.

1 - Not sure I'm a fan of the chancellor being able to override a duke's build orders in order to make ships or agents...
2 - I know I initially pushed for large unit size, mostly because I was concerned about the 40 strong size of cavalry units being too powerful in comparison to the meager 75 spears. (I hadn't notice that the 40:75 and 60:112 are actually comparable ratios.)
But due to wanting to open the game up to people who might not be able to handle the large unit settings, and that the game has issues with unit movement inside cities now the way it is, I think it may actually be better to go with Econ's initial inclination of normal unit size settings. To my knowledge this doesn't change any upkeep costs, I'll check up on that now though.

EDIT - My reasoning for changing the initial tax levels is that drawing the full income from everybody for the first 5 turns really cripples anything we can accomplish for the first 5 turns in terms of independant duchies.