Well it didn't used to be like this, apparently a year ago PNP's had the fast track...
When you look at it PNPs have to do an extra check, in the A11.2 IRCC needs to confirm with the province if everything is OK with the nomination (this is where such PNP as OINP that have minimum criteria like remaining above 400 CRS will recheck to see if the candidate still meets the criteria).
Now, my guess is that in the past CIC were less thorough with the standard checks (like duties vs NOC, funds etc.) that the province already verified, where as now their are being just as thorough with PNPs as with the other classes so since PNP have an extra check they/we take longer.