... You added two chunks of high rain, a chunk of mid rain, a chunk of low rain, and a bunch of very low rain. Everything 75 degrees. Very low drainage with a chunk of very high drainage. Why? And why does it generate flat volcanos?
The rain/drain chunks are for elves and humans to settle.
As far as volcanos go, it's a bit of a fluke that they produce flat, but what it comes down to is volcanos are added after worldgen is mostly done, and as far as I can tell, the height they generate to is chosen arbitrarily, and then the surrounding land is elevated to match. Sometimes it matches with the embark level, and you get a flat one. Sometimes it's under the embark level, and you get lava tubes. Using a low base elevation and fewer volcanos generates more flat ones. If you increase the number of volcanos, they tend to form adjacent to each other and raise the overall elevation dramatically in that area, leading to fewer flat volcanos.
To get a flatter world overall (because some people love perfectly flat embarks) you can designate a small area, 3x3 where that's the only place volcanos can form, and then it will create a mountain where your dwarves can settle, without having to use any high elevation at all. This permits very thin (as in pancake/crepe) worlds, where it can be less than 20Z from embark to magma, far closer than typically having a volcano on the surface (which is almost always more than 20 steps away).
So, while it's true that having a nice big river and volcano on the surface is ... cool, it's a killer on FPS. Having an embark with no surface trees, no surface water, no surface rain, a tiny piece of aquifer for water, and magma easily accessible beneath allows for forts with up to several hundred dwarves while still maintaining >100FPS.
Do you guys really let it run for a thousand years? I cut it off at 75 myself, knowing that it robs me of a lot of legends and world development, because my computer starts to take about one minute per year after about 100. I suspect by the time it reached a thousand it'd be practically realtime.
There's a few settings that let you have longer histories in a few seconds/minutes. The the number of civs, the population cap, and the number of sites. If you only have 4 civs (goblin, dwarf, elf, human) with biomes to match, and under 5 sites per civ, and say under 1000 pop cap, worldgen is quick. If you cull out the uninteresting historical figures, it's even faster.
My 10,000 year 42.02 demonstration world took less than 5 minutes to generate, for example.
However, it should be noted that if you have megabeasts, semi-megabeasts, titans, and very evil worlds filled with dozens of thousands of goblins, getting all the civs to survive to the 10,000 year mark can be almost impossible.
Even with no enemies or evil of any kind, races can still go extinct, even with 3 or 4 civs of each race at the start.