In older masterwork versions I got worldgen crashes like that from switching off and switching back on certain features. Making a fresh install and choosing exactly what features I wanted the first time around made worldgen run fine. Mind, this was a few versions back, could be something else entirely.
I've been tinkering around with my own install of ☼Masterwork☼, though mostly for flavour and my own personal tastes nothing worthy being a true fix. Closest is I've been trying to balance animal populations and frequency. Some of the new animals (often searchable with the -UBIQUITOUS- demitag) had insane population numbers and frequency set to 100 while vanilla animals like the good old grizzly bear were left with [FREQUENCY:2] and [POPULATION_NUMBER:2:3]. The tricky thing is what do you set it to? In my own raw files I've just gone for blatant favouritism and upped the chances of seeing animals I like. Some animals are more equal than others.
I have had a few thoughts on the issue while looking into it: With so many extra creatures is seems worth getting more specific with the biome tags. Instead of several kinds of bears with [BIOME:ANY_TEMPERATE_FOREST], you can split them up into those with [BIOME:FOREST_TEMPERATE_CONIFER] and those with [BIOME:FOREST_TEMPERATE_BROADLEAF]. But then the thing about Masterwork is that there are many options so you could be playing with just vanilla creatures or you could play with all the extra creatures available.
Related, if you've gotten used to playing Masterwork with a certain set of options but then decide you want to try ZM5s creature packs, you'd probably want a higher chance of seeing the new stuff.
There's a lot I still don't understand about how dwarf fortress populates its world and then how it choses which particular group of animals to harass your fortress with. Or answer questions like "What is the ideal predator/prey ratio in the wild and should Masterwork even take it into consideration or just throw what would be most interesting to gameplay?". I just know I don't want to select a huge variety of extra critters for my world only to meet with the same group of Drakes and Asps all the time.