For mud riding I think I would go with carbs, alot less electrical plus injectors and high pressure fuel pumps really don't like getting dirt in them, cleaning a little mud out of a carb isn't a big deal.
EFI for sure. Carbs have vent lines that needs to be routed up and are more likely to give problems. On the Kawies I would say EFI even more due to the 2 carbs they run. Double the troubles. EFIs are also easier to tune. The electrical connections is not a really an issue.
In general efi's have better throttle response and run better in vehicles that are subject to odd angle and rough terrain because they don't have floats bouncing around changing fuel levels with every bump or steap angle.Efi's are also sell adjusting to different altitudes where as carb's aren't.
On the other hand carb's are easier for the layman to tune where as efi's require more knoledge and sometimes special equipment to tune right.
So it really depends on the type of riding you do and your mechanical skill level(or the depths of your pockets to pay someone) which is better for you.