Covering the several of these that I know:
Will the new wound system make megabeasts survive more?
If you mean during worldgen, there's a list item for updating the worldgen wound system, so it'll be different at least and it could hardly get worse. If you mean during gameplay, there's another item for ensuring that hydras are getting the benefit of their unique redundancies. Toady also commented that plain old iron men will be much tougher, so bronze colossuses will probably be really nasty.
Will megabeasts other then demons be able to take over goblin civilizations? Will any civilization be able to be taken over by a megabeast?
Currently, any creature with POWER and a SPHERE is eligable to take over a stock goblin civ, I think (it might have to be from a particular subset of spheres, but I'm not sure). Other civs can be taken over by creatures, such as titans, that have (matching?) spheres. However, it seems like not all SPHERE megabeasts are eligible for taking over a civ -- maybe it requires the CAN_SPEAK tag.
Will "stacked" squads work better? As in, have more of a chain of command then just the squad leader.
Yeah, this list item implies a non-trivial hierarchy:
# Simple specific orders at any hierarchy level from top to individual (kill X etc.)
Will criminals be handled differently? Will there be saner punishments for things?
There's been a lot of talk about beard shaving (as a punishment) finally getting implemented. No confirmation, but it's certainly closer now that we have beards.
Will there be any updates to traps?
Hasn't been mentioned so probably not.
Will crossbows be handled in a more realistic manner?
Attributes, weapon skills, and projectile wounds all got reworked, so they'll probably be different. However, the range and machinegun-like rate-of-fire probably won't be any different.
Will there be more graphics support?
From what we've seen, only in some small ways, like material colors being more widely respected (e.g. the silvery-looking feathertree wagon in the recent dev log screenshot).
Annnd... Are you ever planning to implement multithreading and/or GPU support?
Generally in the past he's said he'd rather do other kinds of optimizations before tackling that.