I'd say there are two reasons why most/all people will experience less fps.
The first reason is that fc2 starts with a lot more detail on by defult, such as high resolution
ground textures, advanced haze(fps killer in fc1) and significantly higher clipping distances.
For me I actually get higher fps in fc2 vs fc1 if I remove all this extra stuff from fc2.(but I
like the new detail levels)
The second reason is that fc1 has been out so long that virtually everyone has installed
some form of fps mods or made adjustments themselves to it to improve fps. Do this to fc2
and you will also see improvements there.
Currently i think I have about the same fps in fc2 as in fc1 after some tweaks, but
a LOT better graphics in fc2 than fc1 :)