It's definitely got its problems. The pseudo-ASCII "graphics" have their charms, but are frequently cryptic (What is that @ sign and what's it doing wandering through the storerooms?!). Recent versions have 3D landscapes, but earlier ones were all on a single plane, and the interface for dealing with the z-axis seems tacked on and hard to deal with. The game is so complex that you really have to read all of the introductory articles on the wiki (especially Quick launch, Starting builds, What should I build first?, and Your first fortress) plus the articles on the basic workshops, buildings, and items, and the one on noise, before you start or you'll find that you've screwed yourself over from the beginning (and remember to always check the wiki on any given building before planning it, so you don't put the only door to the room in a place that's blocked off by the contents!). And it's keyboard-only, which is clunky.
But damn, once you start playing it's hard to stop!
While I'm currently muddling through with my first fortress, I can't help thinking about how I'd plan things the next time around, knowing what I know now about how things work. Putting workshops only a few squares away from the barracks? Bad idea! Walls don't block work noise, so you end up with a bunch of unhappy, insomniac dwarves. Next time I'll go for a sort of "beehive", layered design, separating floors with living quarters from workshops with floors of storage space, staggering the networks of walls and halls from floor to floor for a honeycomb-like structure. Not only will this keep noise away from sleeping areas, but I can also have arrange things for an efficient workflow, so a workshop that produces one good and one that requires that good as raw materials can both sit on top of a stockpile for that item (for example, the butcher shop produces both hides, meat, and bones, so it can share a stockpile with craftsdwarves' workshops for making bone items, one with the kitchen to use the meat, and one with the tannery to turn hides into leather, which can also share a stockpile with the leatherworks, which turns leather into clothes and tradeable goods, etc).
Also: a still is one of the first things that needs to be built. Dwarves are total alkies and require booze to work at full capacity.
And instead of wasting time building fortifications, I need to concentrate on getting things working. Right now I've got arrow loops out the wazoo, but not enough places for my swiftly expanding population to sleep at night!
(For lulz, and to see what got me to check out the game in the first place, see this "Let's Play!" of an earlier (2D) version, by some Something Awful goons trading off being in charge of the legendary fortress "Boatmurdered". It's a laugh riot.)