1. Complex is not the same as complicated. The puzzle should be figuring out what is wrong, not how to get the information about what's wrong, nor how to tell the game what you want to try to resolve it.
2. Something like Clippy is a great suggestion. A newb I helped on my LAN went home, downloaded the game, and got the exact same alligator combat someone talked about earlier. Completely ruined it for him when he couldn't get them to disengage. He complained that so far as he could tell, they'd keep pummeling the alligator until they all starved to death, and rage-quit. At least give some way to walk a complete newb through the menus to allow him to pick up a pointed stick, and when he's ready for it, how to replace that with a real weapon, and how to add armor. 'Course, that wouldn't have helped in this case. I've tried it, and I couldn't figure out how to get them to disengage if I hadn't established at least one person with a weapon ahead of time.
3. Unify zones, for pete's sake. No it's not game breaking, but you need to know that if you want to pasture animals, you use"i", to establish safe areas, you use "w", if you want to store things, you need "p". These are all just regions. Just adding "st(o)ckpile" or "st(o)rage" or something similar to the options on the zone, that enables "O" (capital ''o") to jump to the stockpile settings, exactly like designating it a (p)asture enables "P" and lets you specify which things to pasture, and Bob's your uncle. I'd think even things like fa(r)m plots should be done with whatever you are using for establishing zones. Warrens might have to be something different, since you can specify them across multiple zs, and before excavation. I do understand, however, that those of us who have played for a while are pretty set in our ways, and could never accept the newfangled way of making a food stockpile, now similar to every other zone you would make, "i-enter-arrow-arrow-enter-o-O-f", so you couldn't actually get rid of "p-f-enter-arrow-arrow-enter-ESC-q", but there's no reason newbs should be required to remember three different ways of doing pretty much the exact same operation, and when you use each.
4. More of a suggestion, but among people I've introduced to the game, pretty much everyone is puzzled by the fact that you need a pick to dig through sand. Maybe if those top few dirt layers were diggable without a tool?
5. Context-sensitive loo(k). And merged with whatever(t)is and (q)uery as much as feasible, as suggested earlier. If you are loo(k)ing at a tile, and currently highlighting larch trunk, it would be nice and newb friendly to be able to hit "t" right there to designate it for chopping. If a fisherberry, you can gather (p)lant it. If you are on grass or pebbles or whatever, you can c(h)annel, d(j)ownstair, bCw, bwc, whatever, right there. Maybe only the really common stuff. Ideally, one should want to learn how to do it with keyboard commands because it's heaps faster, so if you were highlighting said fisherberry, it would display something like "gather plant (dp)" so you see the key command every time you use (k).
[EDIT]
Oh, I forgot.
I don't think the problem with weres is that they are necessarily too early, but rather that there are lots of embarks where there's been nothing else to fight, so not only are you thrust into trying to figure out the (IMO) overly complicated military menus, the penalty for getting it wrong is quite severe. And your next embark, your next chance to see what the orders do, it's also going to be against a were.
Like @Shonai_Dweller and others have said, people expect the game to have at least a little combat. Otherwise, why bother with so much detail in the squads, armor and weaponry? It's just pointless complication. There needs to be some early game battles of some sort so the first exposure to it isn't complete and total annhilation.
And personally, I don't think one should expect Wiki or the forums to do the heavy lifting. Most of my play isn't even connected to the internet, so it's not an option anyway. But even if it were, Alt-Tab all the time is hugely distracting from playing the game. Getting through heavy aquifers and moving magma about, sure. Getting through a battle or figuring out how to dig a hole or chop a tree or not cook all your seeds, not so much.
[EDIT2]
Oh, and riffing off something @PatrickLundell said, dump IS too useful to waste on garbage. How about adding different types of dump zones? Heck, even d1, d2, etc. would be awesome, even if there were only a few possible options. Never mind. That's more of a wish than something to make life easier for newbs.