Some interesting ideas here but I think most of them are better suited to options rather than hard-coding.
Many people have scoffed at being able to use points to buy better conditions or get points for worse ones etc... but right now there's a psuedo-system already there (except it's free and semi-random) in the site selection where you can choose your biome and wood availability... There is nothing different from choosing a woodland area instead of a sparse than there is choosing a known metal rich mountain site than a metal poor one.
I think that the ability to tweak starting conditions with a point based system would be a great idea and those who don't want to can go with the defaults that are exactly like what's already there but someone who wants to fiddle can. For example I can choose 2 notches of "increased cave river spawns" to get some points for "pre-scouted ore deposits west of river." or maybe just "2 notches more base metals" or something similar... You have to take a negative aspect to get a positive one for masochists you can select nasty stuff without balancing with good hehe. I could make a list a mile long on both good and bad things that could be added here hehe.
Mainly I'm just saying this isn't something your dwarves are doing it's just a way to customize the gaming experience. BTW the points would be totally seperate from the prepare carefully points since that IS the dwarves doing the other is just tweaking fate a bit for them by the godlike being that controls their destiny (namely you the player) hehe.