I actually make a few edits. Some are just minor quirks like modding down available outfits to just one kind for each race, kind of a racial uniform. So for example, all elves have is robes, slippers and caps. Suitably elfy.
Goblins have masks as headgear, so I made this the only available thing and made them common for them besides helmets, I just like the idea of them attacking and all wearing leering masks.
Other small additions are things like training tags for a couple of things, a few morality/naming tweaks and such. Mostly trying to start more wars, though I'm not certain what effect this has had, if any. [babysnatcher] seems to be the only guarantee for pepetual invasions.
More significant changes I'm trying to veer away from. I don't add 'sand' to every single sandy soil layer anymore, but I do still take out Aquifers. Considering how I like to build my fortress, I just found that voiding large chunks of of the upper level soil and stone as inpenetrable too frustrating to deal with. That combined with frequent flooding accidents, was just too much fun.
The other major change I make is to take out ranged weapons from all races. Maybe I was just getting it wrong, but I had too many instances of perfect military archery from invaders, and then my own forces brainlessly trying to beat things to death with their crossbows and the fiasco that results from this. Especially with wooden ones. So nobody gets ranged weapons, not even the elves. But then I'm not in the habit of provoking the elves anyway. I get most of my wood from trade and I feel little need to antagonise them for thousands of boxes of cloth and reams of crappy wooden swords. I can easily afford any caged animals they bring.