You can build a city under the sea if you start at the coat and dig a tunnel underneath the ocean.
Too Deep conditions are gone. In every single mountain "region", there is a single mountain "local" tile that somewhere under it has some adamantine. If you mine too deep into it, you'll break into a freaky cave complex with all sorts of weird shit- masterwork engravings of horrible things, crushed bone meal and blood coating every surface, babbling and insane humanoids, and other warning signs. If you don't seal it off (unknown if you need to use adamantine, it'd be realistic but I don't think the demons will break the rewall even if it's glass), Demons will come and they're far tougher now. Even a well-prepared fort is in danger.
no boats.
Crops now have outdoor/indoor designations. You can farm strawberries outdoor but they won't grow underground. Plump Helmets don't grow outside. Certain outdoor crops only grow in certain biomes, which is sometimes odd if your fortress is literally located at the border between two. You also can start with Rock Nuts now, just as a minor thing. Oh, and domesticatable camels and muskoxen. The latter appear almost as common as horses and mules for wagon-pulling, so you'll often start with 1.
Soil is pre-irrigated rock, basically. You can farm it without getting it wet, although you have to make sure to make it underground or aboveground depending upon what you want to grow.
Cave Rivers, magma, sand, etc, are no longer guaranteed to occur in any given location.
There's now noble/interpersonal skills. A Pacifier or Consoler can calm down dwarves who are tantruming, a Liar or Negotiator can bargain offers with traders (although not too well at low levels, they must have massive trading skills), a Bookkeeper isn't useful until he sits at his desk keeping records.
Nobles aren't as sucky, their demands are less frequent and they seem to make more reasonable ones in my experience. You can appoint civilian nobles like the Bookkeeper, Expedition Leader (the lesser, earlier form of the Mayor- either your most social or a random (if you picked no social skills) dwarf from the original 7, although he can be replaced)), Manager (you start with him!), and Broker (all 4 of these are the same guy at the start, but you can diversify it later if you wish).
You start with the anvil, no guaranteed metalsmith. If you start without an anvil, you get a whopping 1,000 points to spend on gear but have to wait until your trading noble (I think it's the Broker) cuts an agreement with the dwarven trade liaison they bring now to bring an anvil and they get around to it (usually 2 years or so).
Those are all the things that come immediately to mind, besides rewalling, reflooring, etc.
Edit- Oh yeah- now there's screw pumps (manual or automated), gears, axles, water wheels, and windmills. The millstone now needs a mill unless you build a querm, which does the same thing but is slower. Mechanical constructions in areas with wind (hard to tell now, it appears to be strongest near the sea but present everywhere?) or a river that isn't a brook are now pretty cool. A big use of screw pumps is to move water up Z levels.
Carp are now deadlier than elephants, and Giant Cave Spiders moreso than them. Check the wiki on Carp and on Adventurer Mode for those respectively.
[ November 26, 2007: Message edited by: RubberDuckofDoom ]
[ November 26, 2007: Message edited by: RubberDuckofDoom ]