Here's the questions I can't answer:If so, can I make two different emergency burrows for two different groups of civilians? AKA everyone assigned to this burrow goes to this emergency area, everyone assigned to this one goes to a different one.
Will size come into play more when it comes to damage? AKA, a bolt has to travel through a lot more flesh to get to a dragons heart then a goblin?
Will formations give any bonuses other then simply having your dwarves where you want them? Will they allow you to make your dwarves "face" a certain direction for better combat bonuses? Or are there other bonuses you have in mind?
I will be able to assign certain dwarves to certain burrows, right?
Yes.
Will magabeasts be more dangerous with the new damage system?
Almost certainly. Hydras won't go down nearly as easily (there's a List item to ensure this), and Toady also mentioned that iron men will be more difficult to kill (which should go for bronze colossuses as well). And if that doesn't make them dangerous enough, you'll be able to mod them in much more interesting ways than you can currently.
Will the new damage system effect how often weapons get Stuck?
The entire wounding system has been rewritten, so it'll certainly affect it somehow. I can't say whether they'll get stuck more or less, but they'll get stuck
differently, e.g. it'll distinguish between getting stuck in flesh vs. bone.
How will siege engineers be handled now? Will they still run away from enemies?
This came up a while ago. Sounds like it won't be changing yet:
Any ideas to incorporate siege operators in the military, and making siege weapons more useful overall? Well, siege weapons should have a role in the military, at least its what i believe in. Making them more useful and incorporating the new squad system to siege operators and maybe linking them to levers and pressure plates would make them a blast to use.
There's an overall vehicle rewrite thing planned for some point during the overall invader improvements. This'll likely change everything about fortress siege engines and establish some more structure on the associated staff. It's not the farthest away thing in the world anyway, since invader improvements are one of the things on the plate for after this release. The vehicle rewrite is one of the more ambitious parts of that, though, so some other invasion changes might be coming in first.