There are many differences including:
Noise: wood is less noisy when fired
Recoil: wood has less recoil
Strength: wood is stronger
Durability: wood can take more abuse
Flooding: wood never fills with water and sinks
Finish: wood can be refinished if desired
Customization: wood guns can be customized easier to your liking (you can drill holes anywhere)
Tracking: Pipe guns track a little better because they are thinner
In general, a well taken care of wood gun will outlast you. You may need to change a spring in the trigger but not much more.
In reality, assuming normal wear and tear, both type of guns will work fine. Wood has more advantages but you pay more for them. Call it personal preference.
BTW: If you are paying $1,200 for a custom wood gun you may want to shop around. You can get a Hatch, Koah, Blacktip, for less than that. Unless you are getting a quad roller tuna cannon.