I know I'm looking for answers to my big question: If you join a guild that requires you to do criminal acts (the Thieves' Guild and Dark Brotherhood) while part of a non-criminal guild like the Imperial Legion or the College of Winterhold, do you get kicked out of non-criminal guilds if during a quest for a criminal guild you are caught in the act? I know that in Oblivion I killed some Daedra worshippers only to learn they were Mage Guild members when I was kicked out of the Mage's Guild for assaulting them. Hence I did criminal guilds early, to get my criminal history out of the way and then get back on the straight and narrow. Once I was at the top of the guild, I didn't need to really worry about committing crimes, since I generally didn't steal or murder unless it was necessary to proceed.
Also, if you join the Legion or the Stormcloaks:
SpoilerYou'll lead an attack on one of Skyrim's cities, which one depending on your affiliation. Will you still be able to do local quests in the attacked city after the faction questline is over, or should you do those first before the place is destroyed?
It's like Fallout New Vegas where I was trying to juggle each faction so I could maximize quests without barring myself from access to anything.