First off, what versions are you trying to move between?
Copying my save from 0.40.03 to 0.42.04, it loaded without apparent problem. As mentioned above, many of the new systems weren't available - no bookmaking/papermaking stuff (neither the recipes nor the labors), nor instruments (since my civ didn't have it at worldgen). But it was still using most of the new mechanics - I could define locations, hire people into occupations, dwarves would tell stories in the inn (the riveting tale of how at the founding of the fort, my expedition leader became an expedition leader! :p No one has any dance or poetry - I wonder if they'll develop that, or if they'll stick to other stories) , they used the new thoughts & preferences system, etc.
Looking in the error log though, it did run into problems. A couple entity_default.txt errors that it seemed to be able to work with, converting around some stockpiles and site pops, and then it has a bunch of "*** Error(s) finalizing the creature <yadda>" (one or more "undefined local creature material set to <yadda>" each). It seems to have been able to resolve all the issues, at least with automated workarounds (e.g. fluffy wamblers now have tallow, leather, fat, and hair - not vanilla, but not horrendous). I'm guessing there's something more specific about your fort (or lucky about my fort) that's causing the difference. Did you do any extensive raw customization in the old fort? Maybe post more of the errors its giving you?