Projector its basically a reflector which is stock.
Everything is technically a reflector.
Projectors reflect light out of a lens to a specific pattern
Reflectors still reflect (obviously) but it kind of scatters it, there are some E-code and such housings that can house a HID properly without scattering the light, but projectors are far more precise, I guess you could compare the light of a flash light, and a laser pointer, one is aimed and precise.
Since there are no headlights for the WJ that I know of that are a reflector for HID, you should go with a Retro fit, I do know that there are Projector headlights for the WJ already made, but I am fairly sure they are Halogen, as the bulb type is not D2S/D2C or D1s or D3s or D4s, Correct HID projectors do not take anything but D1,D2,D3 or D4 bulbs, I believe.
Just to sum up.
Stock = More light with HIDs, but no more on ROAD than before.
eBay projectors = More on road, but not correct, could have future problems.
Retrofit = Great output, no long term problems.