@George_Chickens: Lowering the general invasion threshold to 20 is easy: just set the progression trigger for invasion pop to 1 = 20, rather than the default 3 = 80 [2 = 50] in entity_default.txt file for the races you want to be allowed to invade you. (Semi) megabeasts similarly have triggers in their raws (individual per species). FBs, necros, and weres are outside of player control currently, as far as I know. The available triggers can be changed by changing the copy of the appropriate raw file in the save (not the original the save raws came from) in between sessions (don't change a lot of other raw things in the save without knowing how the game reacts).
Other newbie issues:
- (Mentioned before) Realizing that you need to build a down stair or up/down stair at the target level takes some getting used to. I guess you can consider a stair just up to the level of a 2*2 meter hole in the floor above (i.e. having to reach 1 meter to in some direction to heave yourself up while carrying a boulder) to be rather tricky to deal with, but you'd need to form that kind of mental picture to understand why you need the "extra" level.
- Building from ramps/stairs diagonally: "I can swear I saw the dorfs build both the wall segments to the side of the ramp while standing on it, and I've seen them build diagonally before, so why won't the #*! build the last segment!!!"
- That there is an inexplicable but important difference between carved and built fortifications, and why it matters (hint to those who don't know: there's no protective roof/floor over the built one, so you can't walk on it but critters can get in [and I think X-bow dorfs can climb out to make suicide charges]).
- How drawbridges work, their magic ability to fold many tiles long bridges up to a single Z level high wall (without a roof). Other counter intuitive features are that open retracting drawbridges get smashed when you drop cave-ins through them (though that's hardly a newbie task), that trees grow through them, atom smashing (and when it doesn't work), when bridges are magma/fire safe and not (and that this sometimes is dependent on alignment), etc. A retracting drawbridge is, after all, one of the first defensive measures a player ought to learn how to use.
- That dorfs don't know how to build walls, i.e. that the overseer will have to micro manage the building of walls either through the building of access scaffolding to all parts of the new wall or through building orders issued with the right timing (i.e. such that the previous section is actually going to be built before the next one).
- Building destroyers, and what can and can not be destroyed.
- Stockpile links. That they should keep away from them until they understand them in detail, and then only use them when they have a specific reason to do so. One of the most common reasons for "Why are they producing booze, I've got everything they need in abundance" and similar issues is failed linking (typically no link to barrel stockpiles, in this case).
I don't know how to improve the situation, although I guess trying to issue orders that are made impossible by linked might possibly be indicated to the player.
- Bin/barrel related workshop order/manager cancellation spam. The default recommendation will have to be to avoid bins like the plague until it's fully understood when they're safe to use (or they're revamped so they can actually be used in a reasonable manner even by newbies). The same goes for barrels, but, I think, to a lesser extent.
- Having randomly selected but occasionally important dorfs murdered by the injustice system as scapegoats for the overseer's failure to fulfill nobles (sometimes literally impossible, given the resources available) mandates, as well as the overseer's inability to predict nobles' trade bans before they're issued. I assume the Villains release will have to deal with that kind of problems as it seems a somewhat working justice system will be necessary to protect your fortress from plots, so you won't be able to just make sure not to enable it (and newbies wouldn't be expected to avoid what seems to be an important feature).
Proposal:
Tool for troubleshooting some of the inevitable "why won't my dorfs to X" pathing issues: A path finder where the possible path from a selected location is painted (like the trade depot one) to allow users to find where the path is broken. Can probably be implemented with DFHack, but that won't help vanilla users.
Edit: Therahedwig's point is a good one. Getting a dozen migrants to assign jobs to (and try to make rooms and beds for) gets a bit long in the tooth, while monster waves of 30+ is a real pain (I manually up the pop cap to the current pop + 10 after each wave until I've reached my target level, but that's not something you can expect newbies to do).