Q2E had a very different approach than PB2 does. Q2E was about enhancing Quake2, and Quake2 alone. The engine was completely reorganized and no longer supported mods. It was also geared toward high-end machines, and eventually went to a Doom3/Quake4 style rendering. Paintball, on the other hand, attempts to maintain backwards compatibility and support for older machines.
In short, the only thing keeping me from using Q2E is months and months of hard work.