Same here... I use the IDE built into Proteus, and have for years.. I just use the IPE for chip programming, even that's on its way out as I have one of those TL866 II and it does all the chips I need.
Never really got to grips with MPLABX just didn't feel right..
I don't know if this tool will replace the PicKit3, but I found it when I saw the notice of discontinued support. For only $15, it seems reasonable if it can replace the capabilities of the PicKit. Seems to me like it does.
So here is an example of who this hurts .... The company that I used to work for deals with custom industrial automation where we have several hundred embedded micro's (all programmed in MPASM) running on various platforms and various machines out in the field throughout the world. I can tell you, that they are not about to migrate all of their software spanning years of development "moving forward with the times" to the latest and greatest because some bean counter at MicroChip realized they can remove a LEG and still survive, not fully understanding the fundamentals. It's only a matter of time before the other leg is removed before you realize there is no foundation to stand on.
I am still using MPLAB 6.05. and have not used many older PIC devices in recent years ,I have 2 PK3 for PIC16 etc that need high voltage programing. although i have a box full of them I started with PIC16F84 and PK2 in assembler, seems an age ago now, ! Snap is a good low cost programmer with its limits as mentioned , I have also got a couple of curiosity dev boards, with onboard programmer, ( PIC 18F57Q43 ).