1: Now things have ethics and aren't just our thralls, it's kind of better, even if I do want to display goblin totems all over my walls.
1/
It would be nice if butchering for bones was a separate ethic than butchering for meat. I don't want to turn my dwarves into sentient eaters just to get goblin bones. (And butchering goblins for bones seems perfectly ethical from a dwarf perspective to me).
And the really annoying part is, that ethic doesn't work well in practice. From what I can tell, when you have those ethics set (EAT_SAPIENT_OTHER, EAT_SAPIENT_KILL, MAKE_TROPHY_SAME_RACE, MAKE_TROPHY_SAPIENT set to ACCEPTABLE), you can still only butcher nameless generic sapients ("Goblin Lasher", etc), not anything with an actual name ("Song Nguslutuz, Goblin Swordsman", etc). At least in my experience, virtually all hostiles that show up will be named critters nowadays - your only real hope of butcherables is /sometimes/ undead will show up as un-named generics, and sometimes those corpse-corpses will be butcherable.
6. Setting up burrows for civilian alerts isn't much work. You designate one corner of the map at the level below ground, step down until you can't get further and go to the opposite corner and end the burrow there to get one for the surface. You may need to do some minor adjustments to remove the bottoms of pools and the like, and you may need to add a small bit of surface if your fortress has a surface component. It's the same with burrows for caverns: mark everything, remove the cavern levels, add back the parts that are inside the fortress.
It's annoying and impressively time consuming when they cover a lot of z-levels (though admittedly you only have to do it once, if you're thorough), so you're trying to mark strips of hillside in tiers all over the map, and then again for each cave level. And if you add some new outdoor superstructure or carve away some mineral patch, but forget to update the burrows, you can easily wind up with some very frustrating, befuddling 'misbehavior'. Ultimately, this is a key reason why I've favored mostly-flat embarks lately. (my favorite is sharp-cliffed hill surrounded by flat plains, but that's hard to find)
That said, I still find it better than the old 'outdoors' system, but that might be more about using the old system when I was relatively new to DF, so everything seemed more complicated and prone to undesired behaviors.
For the specific original point about wood, the 'o'rders menu prohibition against wood gathering can be a useful stopgap. It'll also break internal woodhauling between stockpiles, but that's often a worthwhile trade to keep your whole fort from suiciding in pursuit of that willow logs they mistook for a XXpig tail sockXX.
Also: how do you get dwarves to get married these days? >.<
Forced isolation together seems to be nearly required, now. Dwarves have a lot more to occupy their downtime with, and they seem to skimp on a lot of the classic bonding time. Most successful modern marriage forts seem to involve long periods of zero labor for large chunks of the population, or locking prospective couples into tiny rooms to force them to see each other, with no possible activities beyond idling or interaction.
There's also that thing which controls what percentage of the population is allowed to be children/babies, so maybe that is blocking pregnancies in your fort?
That's BABY_CHILD_CAP, but it defaults to being very liberal: [BABY_CHILD_CAP:100:1000], limiting you to 100 babies+children, and limiting you to 1000% of your fort being babies+children.