Alright I don't know how much this has been brought up, but I'd like to get my own ideas about a few pet peeves of mine out in the open.
1. The handling of time makes for some bizarre things that often get to me in this sort of game.The way that everything is balanced time wise is simply atrocious. Having an entire year go by in 1 hour is way too fast for the scale that Fortress mode takes place at. I'd personally prefer that the game be balanced more around hour long seasons or even 1/2 hour long months. This may sound extremely slow, but Dwarfs are already taking completely undwarfy amounts of time(far to long by tick break down) to carry out certain tasks. No Dwarf would take days to move a single stone. When it comes right down to it, every action needs reassessing as to what portion of the arbitrary time units they take up.
2a. I already said in a relevant thread that I fully support enemy tunneling. The thing is that the whole mining system is currently far to simplistic. Dwarfs as a matter of record have an innate stone-sense, this dose not however mean that they should all be able to identify every type of stone, ore, and gem deposit that they find on sight. I would suggest the addition of Geologists whose job it is to identify the type and quality of the stone. They would also determine whether or not a section is safe to dig into. Yes I said safe to dig into . I see cave-ins as functioning to ways: 1. As a percent chance during mining modified by digger skill and traits (goblins are stupid, chaotic, and have short attention spans so they would meet with hilarious disaster quite frequently.) 2. As random events with likelihood being tied to material and how the strata are layered in a given area. These could be triggered by nearby mining, heavy foot/wheelbarrow/mine-cart traffic, and or seismic activity.
2b. The subterranean world is far to boring. Our Dwarfs, like real Dwarfs should need to really put their ingenuity to the test. Natural caverns of varying size, shape, and contents should be randomly distributed throughout the underground. The current cavern system should star more around level 50 an should function as an Under-dark type region complete with it's own playable races making surface conquest a possible goal. there should be natural fissures an chasms of varying scale that you will need to account for. Support structures should be mandatory instead of being used simply as trap triggers, giving a reduction to the chance of a cave-in.
I've been at this for a while now so I'll cut it off here, gather my thoughts, and return when I have things to add.