You can change PPS on the fly, no problem. No reset needed. I never wanted to do a USB on-chip version, but tons of people pushed for it and I was stupid enough to follow the crowd instead of being the dictator of my project.
Its more these problems with v4 (all suck vs suck):
1. USB stack unstable, unmaintained open version vs closed unworkable undistributable microchip version
2. Speed sensitive things (SPI/I2C sniffing) take a huge hit on v4 due to USB overhead and lots of support questions about these
3. Development with active USB is a PITA, impossible to single step problems with any reliability
4. The extra flash in the PIC is (as i recall) not that easy to work with. You start to need stupid compiler tricks and stuff to address the top of it
We have a v5 with an ARM chip, but its so much more expensive - and - once we get enough flash to be useful, super more expensive (plus no PPS) :)
Currently, we are done with a redesign of the v3 using the cheaper, smaller FTDI x chip. It fits in a 5x5, and we're making a milled aluminum case for it. Slick, anodized black square with 1x10 pinout and laser etched labels on the pins.
I do like your idea of using a cheaper PIC instead of USB and making a parallel interface, that might get us somewhere, especially with a bigger, cheaper arm sans USB.