Evil worlds and non-breeding dwarves.
You can't edit the randomly generated effects, but you can disable them and create your own. There are options in the advanced world generator to set the amount of randomly generated rains, clouds, and many other things. Setting them to zero will disable them, while still using the player created ones.
Civs can be prevented from spawning in a few ways. Go into the file called entity_default.txt, that's where all of the entities are. You could outright delete non-dwarven raws, but it may be easier to instead remove certain tokens that control where the civs spawn or what site types they like, what their populations are, or what creature belongs to the civ.
Necromancers are a bit more difficult, as towers aren't controllable in the raws. You could make more necromancer secrets, and give them more spheres that just death so that more gods can grant that blessing though.
To help you figure out how to make the weather and necromancer interactions, check out the folder within the raw folder called 'interaction examples', which has files to show you how to make things such as were-creatures, vampires, necromancers, and evil weather.
For dwarves to reproduce, they must be married. If there are married couples and they aren't reproducing, then I don't know what to say. You may just not be waiting long enough, or they may be having miscarriages. That can be caused by things such as starvation, dehydration, or injuries.
My militia commander seems to prefer bashing enemies with his wooden crutch instead of impaling them with his masterwork spear. Is there any way I can get him to swap out the crappy crutch for a nice heavy metal one?
Have you tried forbidding the crutch in his inventory? You could also try marking it for dumping and place a garbage dump somewhere nearby. Then just forbid all non-metal crutches so that he can only choose a metal one.