My experence with MPLAB X is in general dodgy IDE. The only thing I read on the Microchip forums "if you are not using Linux or Mac in your workflow, use MPLAB IDE". In short, MPLAB X:
- It has been sooooo slow, from day 1. This inherent to MPLAB X, because it uses netbeans crap. I have got the same hatred towards Eclipse, they both run in a Java runtime environment.
On my laptop (an C2D system, 4GB RAM, 128GB SSD), I boot MPLAB X, half a minute later there finally is a IDE window. CPU was utilized 100% all the time.
On my PC (a new i5 system with 16GB RAM, 256GB SSDs) I boot MPLAB X, it still takes 20 seconds to boot and 100% CPU utilization.
Anytime the IDE goes "parsing projects", it becomes unresponsive for a second or 2.
If I "Clean project" on laptop machine, it becomes unreponsive for a second or 3.
People recommended me to delete/replace the "xlcm.exe" because even in the FREE version it is contacting the Microchip server on every file being compiled. This "contact" takes like 2-3 seconds if you're unlucky. So a medium sized project with 20 files takes like a minute extra (!) to compile.

On my PC, after replacing the xlcm, enabling parallel compile, that same project takes 4 seconds to clean&build.

Why isn't there a decent IDE written in Qt these days? Qt runs on almost everything , should be possible..
- MPLAB X uses so much memory. Because it runs Java.
- PICKIT3 & PICKIT2 support is shabby. It's not a case of it either works or it doesn't work. It's mystifying, unpredictable, MPLAB X crashes randomly, undocumented errors (like, I don't give a toss that MPLAB X misses a memory object, I want my debugger to debug this chip).
I usually end up using the standalone app with my PICKIT2, and only when I really have to start the debugger. Or go back to MPLAB IDe. MPLAB X & PK2 support also has many bugs, but they say it's not their top priority to fix the support (because PK2 is old..).
I
only have had problems with PICKIT3 and PIC24FJ64GC006 (one of the very latest ones) in MPLAB X. Never got it to work. MPLAB IDE? Some issues, but it works. The debugger glitches out every now and then though, which is extremely annoying.
I have got a feeling I made a step backwards whenever I'm using the PK3 in comparison to PK2 (except for extended device support).
In my opinion Microchip should really try harder and fix their tools. I think their range of 16-bit & 32-bit micro's can be really interesting, there is a lot of "content" out there to be sourced from, but it's too bad there is so much toolset (especially on their software side) crap going on.