I like PS2 for my gun games. It can get a little tricky since some games use different guns, but it runs smooth as silk.
Recently I've been going back and forth trying to make a decision about this myself. I had a Turkey Hunting USA cabinet I picked up last fall in a cab lot that's been gathering dust. Cab was in great physical condition with a nice 27' monitor but had no guns and the flyback needed replaced on the monitor. Initially I planned on repairing the monitor (or replacing it with a 27' CRT TV) and putting in a Playstation-to-JAMMA PCB. Combine that with a PS2 with hard drive and some third party guns that are Guncon/Justifier compatible and I could play the entire PS1 and PS2 library without changing guns or consoles. Be able to play a few PS2 Atomiswave ports is icing on the cake.
In the end though I ended up doing the complete opposite, grabbed some Amtrak guns, yanked the out CRT for a 24' LCD monitor, used a CGA-to-VGA converter board so I could hook the PS2 up, and I also added a PC for emulators.
The main reasons I decided on LCD + Aimtrak over a CRT with Guncon/Justifier was software. With the exception of the Time Crisis: Project Titan every PS1 gun game I really liked was an arcade port (all of which are superior in MAME) plus there's quite a few arcade emulator exclusive games. I definitely prefer the Guncon's preciseness and ease of use but the amount of additional games supported by the Aimtrak coupled with a cheap PC make up for the inconvenience.