Masterwork DF and Dark ages: War & Mythos use a script for random generation. I know MWdf has it configured to be able to do a number of things, including generate a number of sapient creatures that show up in adv mode.
http://www.bay12forums.com/smf/index.php?topic=91255.0CreateObjectBut if you really want to use this mod in fortress mode, it's pretty straight forward. Assemble your dwarf fortress of choice; modded or not or whatever, drop this mod in, pick the playable civ you want to replace from an entity_ text and replace the CREATURE: entry with the all caps of the species you want, then edit the species you want to play to have whatever you want of the appropriate tags you can probably copy over from the civ you're replacing from the respective creature_ text. [INTELLIGENT] and [EQUIPS] and [CANOPENDOORS] for example. It's also safe to delete all creature_ texts besides the ones that came with this mod, and all the entity_ texts as long as you make sure to have at least one entity_ text with at least one civ inside it, else worldgen might not work.
It works, for the most part, though you might need to copy over the gaits if you notice any weirdness. (for instance, if you use Clefairy you might notice they move really slow respective to dwarves.)
Some species are pretty weak compared to others, and make for incredibly challenging fortress embarks.
Some species don't seem to survive as civs often in worldgen; For instance, almost every worldgen I've tried with Ghastly as a civ ends their entire species within the first 30 years.