A couple of things come to mind off the bat:
- Aquifers are dumb. I never play on aquifer embarks and don't see the appeal in them either. This is a diggy-fortress-buildy game. Having your new digout flooded right away is obstacle #1 and will result in "what the hell?" moments. Consider making aquifers a default-off option in worldgen.
- Evil biomes and undead generation is unreasonably, weirdly overpowered and I think their current mechanics are more or less an oversight because it was deemed "an error funny enough to leave in".
- The interface. At this point it's a meme and a trope and we all love to hate it, but having this monolith of key combos around is obstacle #2. It isn't so much that it's not efficient, because it can be quite efficient once you get muscle memory. The problem is that weird, fringe, sub-menu options are not evident even for seasoned players, like the various sub-sub-menus of the (o)rder menu for example. Or the arcane intricacies of the (N) and (h) menus. Also it would be a big help if the main (Tab) overview was sorted into functional groups, rather than having all the shortcuts in one pile.
- Unnecessary complexity in parts. This is not so much a newbie obstacle but it is a massive obstacle to players in general. Why are there endless pages of various leathers and bones littering the selection screens for military uniforms and other things? Condensing these down to meta groups of just 'shell', 'bone', 'leather', 'wood' etc. would not hurt, because I have not seen a single instance where I thought "Boy, I'm feeling literal and would really like to get some Aardvark leather armors made. There better not be any Yeti leather armors in this pile or I'm gonna throw a tantrum!" Similar to this: Browsing for building materials is a chore. Why not a meta group selection beforehand, letting you decide between 'stone', 'wood', 'metal', 'etc' before the player is thrown into more endless pages of lists? Why not make the lists and sublists alphabetized?
Don't agree that managers / bookkeepers are essential for the survival of a fort. I do quite well on mine and never rush these jobs.