Currenly the fractional part of Primecoin's difficulty is highly non-linear. The integer part is not proportioinal actual mining difficulty, either. I wonder if ypool could come up with a proportional difficulty so that when it increases we see proportional increase of actual mining difficulty (i.e. how many machine hours are used to find a block). A proportional difficulty is useful for miners to estimate return.
Ypool has a statistically significant sample of workers. One could multiply time-per-round by the total share values for the round, then time-average the result to get a proportional difficulty index. Because share values are assigned artificially to different chain lengths, sub-indices can be made by substituting total share values with total 6(or 7,8,9,10)-chain numbers in the round in the calculation.
I don't know how this index is related to the integer part of Primecoin's difficulty, though.