This game is AWESOME, and the complexity is very much part of what makes it special and draws players like me to it. That said (and we start with the obvious of course):
1. ASCII (and im an old MUD player). Get an official tileset. Make it easy to change ingame (see minecraft) when people get that far.
2. UI. Needs mouse support. Menus need to be consistent and more clearly organised. They need to be more consolidated and easier to get thru.
3. World creation.. make more obvious toggles, like "volcanos" or "aquifiers". Aquifiers themselves are horrendous as they stand now, they spam the whole map and are a horrendous trouble to even experienced players, and you have to edit game files to fix them. I had to google to find out what "embark sites" really meant.
4. General unit oversight.. one of the most overwhelming things for new players is there is NO (obvious) way to quickly see how things are running.. you have the limited jobs menu, the messy units menu, and 3rd party dwarf the rapist, which in itself is a good start but not quite up to par. Just finding your guys on the map can be horrifying, especially if you are trying to dig thru the alerts menus.
5. Military. Sort out uniforms, training, and all the assorted bugs. Make it easier and more transparent/obvious how to control them. This is major.
6. General bugs and game balance. FPS issues and justice, for two big examples.
At this point, I would say it is a good time to stop pushing forward, take a big breath, and go back in to the core of the game and clean up shop. Streamline it, make it nice and im sorry to say, but more undwarfy. Leave the dwarfiness to the actual dwarves (which i wouldnt change for the world). If it doesnt get the knots and kinks out at this point, it probably never well, and you will end up with a bunch of wonderful ideas getting lost and broken on the tangled mess in the middle.