Hm, dunno, been awhile since I last changed it ALL out from scratch. I shall do so now just for you, and report the things I would change:
1) Embark points: 10,000. I may or may not want to use more than the standard allowed embark points for any given game. But this setting being low FORCES you to use few points. Setting it to 10,000 means later on, I can decide per-game how many to allow myself.
2) Year to begin checking dead megabests: 10,000. I see no reason to force the worldgen to stop at this arbitrary point. Just keep going forever and let me manually stop when I feel like it by hitting enter.
3) Cull unimportant historical figures: sure.
4) Temperature: 0 to 100 instead of 25-75. I am not a big fan of temperate biomes *shrug* Sometimes I'll even set the mesh (later pages) to 3 2 1 2 3 or something.
5) Volcanism from 1-100 still, but changing both the X and Y variances to 3200. This makes volcanism individual world tiles vary from 0 to 100 instantly from one to another, maximizing your chances of getting sedimentary and volcanoes near one another. I suggest NOT using the mesh for this. The mesh has a resolution of 2x2 world tiles minimum, whereas this gives you variance on a per tile basis.
6) Other mins and maxes I don't touch unless I want a wide selection of some particular biome. Like if I want a glacier world, then high drainage, etc. Usually default though.
7) Mountain peaks - usually lower than what it has, because who cares? All it does is potentially reject good worlds for peaks that you can't even embark on anyway.
Volcanoes - set very high. This number can be absurdly high and they will still only take up a small portion of the world, giving you options.
9) Mineral scarcity - usually lower, sometimes higher. Depends on desired challenge, or if I want big empty sections of stone for carved out megaprojects with color consistency, for instance.
10) Titans and stuff - usually increase. Titans are fun! And more potential for amusing legends and adventurer mode stuff.
11) Number of demon types - increase. More potential for webbing ones or other useful or interesting critters in case I decide I want to try to harness their power. or make demon silk socks.
12) Number of bogeymen types - zero. Stops bogeymen in adventure mode which I personally find silly and godawful annoying.
13) Good and evil desired tiles - all zero. I am not a fan of good an evil biomes. If you like them, though, tweaking these is great for determining whether you just get tiny pockets, or huge oceans that are all evil, etc.
14) Minimum initial counts - ALL zero. These do nothing to actually make the world like you want it. They only reject worlds if they don't randomly qualify. You can make your own choices, I say. And if you want to alter outcomes, the much more effective method is changing min/max temperature, drainage, etc.
15) Erosion cycles - 800-1000. Guarantees no dumb looking rectangular computer gen mountains.
16) river counts - 400 or 800. It won't actually make 800 rivers. It will just do the maximum it can fit reasonably, which is what most people probably actually want.
17) Cavern layers - 2. 2 guarantees all plant types, but slightly reduces lag I assume.
18) Cavern openness and passage density - mins and maxes all zero for all 4 entries. Guarantees large open caverns that are less laggy and also allow more interesting settlements, IMO.
19) Cavern water - min 30 max 30, like to have some water. It's still not actually guaranteed, depending on your embark site.
20) Z levels - I add a few at least to each entry. If I plan on maybe making huge underground cathedrals or something, I'll choose one of the layers and add a whole load of z levels here to guarantee a large uninterrupted building area.
21) minimum number of ___ squares - again all zeros. See #14.