I have recently switched from MPLAB 8.something and C18, to MPLABX 1.6 and XC8 compiler. I am using genuine Pickit 2 and the target is PIC18F4553.
I have noticed that it takes MUCH longer to enter debug mode (i mean compile, link, program mcu, enter debug mode) than old MPLAB did. Have you also noticed that? Maybe there's something wrong with my hardware (it's rather old, but quite capable)? I especially see difference in compilation time.
I like XC8 much better than C18 (normal interrupt declarations! at last!), but this is somewhat annoying to wait for like 10-12 seconds for debug to start, while in old MPLAB it used to takes like 6 seconds or so.