Primarily for me it's the compile-program-debug/run step as I mentioned earlier, it's soooo sloooow in comparison to the old school, but tightly coupled, MPLAB 8.
Secondly it was the sheer bugginess of it. I would forever be having problems with debuggers, but they seem to have cleared that up about a year ago. Not before time though.
MPLAB 8 has it's character building featured too of course, but productivity-wise, particularly having used it for many years, I prefer it, although slowly but surely it is being marginalised.
XC8 is buggy, but XC16 and XC32 are reasonably good. I can't say I've found a compiler bug in XC16 or XC33 in some time. The same is not true for XC8 where it's not uncommon for it to spit its dummy out. However, before XC8 I used the Knudsen Data CC5X and CC8E for PIC16/PIC18, and more recently C18 for PIC18. With the Knudsen Data compilers you have to do a lot of work yourself, including taking care where your data is stored in what RAM bank. They also couldn't deal with anything more than very simple arithmetic in single statements. C18 was better but only supports PIC18.
The whole physical debugger interface thing has long been a problem for many vendors, particularly when many were parallel port based, and the move to protected mode operating systems. With USB being so ubiquitous, and with it being so mature now, it seems crazy that there are still problems in this area, but regretfully there are. Lots of random plugging in and unplugging, fannying about with reinstalling drivers, rebooting the computer, you name it.
The RealICE, ICD 3 and PICkit 3 all need their various firmwares being updated when you switch cores or between MPLAB 8 and MPLAB X, and in the case of RealICE and ICD 3 you need to switch drivers too if you switch IDEs. Sometimes you even need to manually upload the firmware to make the debugger work. It's yet another time consuming and ultimately badly thought out design from the vendor.
But as I've said many times before, this all pales into insignificance compared to the PIC32MZ silicon releases and Harmony Framework, 18 months since release and still a year away from being useful in production, coincidentally much the same timeframe as MPLAB X.
Having said that, I do love some of the newer peripherals on even the PIC16s, but they can take some learning.