alright, thanks people. I'll try the region thing. If you make a region instead of an island does it prevent any of the lakes being saltwater?
I have... actually never made an island map. o_0 As far as I've seen, whether your lakes are freshwater or saltwater seems to depend on the world seed. Regions get oceans and saltwater lakes, too.
I haven't tried it, but AFAICT Aquifers tend to be attendant on lower elevations & proximity to map visible water sources.
So when genning your next world, I suggest: No Oceans, Higher Minimum Elevations, nullifying the Required Low Elevation Subregions setting, & possibly lowering Maximum Rainfall.
& Don't embark on Oceans, Lakes, Rivers, or Streams (Brooks seem to be ok).
Note: Sand or Sandy soil layers seem to be especially prone to Aquifers, IMAO.
You're definitely right about some soil types being prone to aquiferliciousness (conglomerate, I don't think it even exists without aquifers, but sand, peat, and sandstone are bad, too).
Lakes can be hit or miss--sometimes you'll get a perfectly dry and cromulent sedimentary layer on the shore.
Depending on what kind of embark the OP is looking for, I've had better results setting meshes to 2x2 and weighting things towards the medium range (40-60), maxing out the number of subregions, and taking out ocean/desert/etc. minimums altogether. No edge oceans.
Screwing around with height and drainage gave me big problems with human/elf/kobold survival in 40d, though it doesn't seem to be
as bad in 2010.