Yes I have been using PK3 for about a year now, and I am quite impressed with it, I use this extensively for my R&D projects and production items.
But I have not used PK2 so cannot give a detailed comparison of the two products.
I think the main reason why people find fault is that there were some differences in the two products, and most people were used to PK2 and found PK3 un-familiar, also some bugs were found in PK3, but these bugs would not cause any problems for you.
PK3 works very well with MPLAB, I also use CCS compilers, PCM, PCH and Hitech C compiler (Lite), these have no conflict with the device.
---------- Post added at 07:14 ---------- Previous post was at 06:50 ----------
I forgot to mention, there is one small problem though, but not a serious one.
Sometimes when PK3 is connected to the computer via USB, MPLAB detects the device but fails to load the device correctly (but device always loads correctly in Windows XP), to make MPLAB load PK3 correctly, select either another programmer like PICSTART plus, then re-select PK3, or select PK3 as debugger, then re-select PK3 as programmer, this makes MPLAB load PK3 correctly.
The actual error is something like this.....
PICkit 3 detected
Connecting to PICkit 3...
PK3Err0033: 4 bytes expected, 0 bytes received
Failed to properly connect to PICkit 3
I posted this workaround in Microchip forum. The first time this happened I was worried that the device was defective, but the above workaround solved the problem. The above workaround is not a permanent one, and needs to be done every time MPLAB loads PK3 incorrectly. I have no idea why this happens, but maybe the problem has been sorted out in the later versions. Apart from the above bug, the hardware connects flawlessly with Windows XP (and in my case also Ubuntu).
When buying make sure you get the latest version, I think Microchip supplies the latest versions of their products, unlike other suppliers... but I am guessing here..again
Please also note that I use Ubuntu as my main operating system, with Windows XP running in Virtual Box, all my observations pertain to these environments only...
It is very likely you may have a different experience than mine if you are using OS like another Vista or Windows 7...