The biggest problem I've had is flight paths. Things don't fly well in QW, so a lot of weapons that use projectiles end up being very aggravating to code or use. This is also why the AirQuake team chose not to make a QW port.
I'd like to make more QW mods though because QW runs so much better for net games, and I like playing against friends and setting up games on IRC. NQ just won't do it.