I have the Bad Boy Elite with the Kawasaki and a 54" deck. Price and dealer were the deciding factors. It has been a tank so far. Only one problem solved under warranty.
I was set to buy the Kohler with a 60" deck when the owner's daughter, who works at the dealership, came out to talk to me. She went to school with my youngest daughter and I always talk to her and her little ones. She said I would be better off with the 54" deck because the 60" tended to scalp the yards on rough ground. She also said the Kawasaki would outlast any mower and used a LOT less gas. I took her advice and have been well pleased. Mower starts quickly, sips fuel, and gives a great cut. I agree with dragoneggs on the Kawasaki. It is great.
My last mower had a Kohler Courage engine. That is supposed to be a 500-hour engine and sure enough, at 502-hours it self destructed into a pile of junk.
Something that people sometimes ignore is seating comfort on their mower. The Bad Boy is comfortable for my wife and OK for me. Sit on both mowers and see which feels best.
Perhaps the one single item that made me buy the Bad Boy was the electric deck lift. My wife loves to mow, but is short and had trouble changing deck height on our old smaller mower. The Bad Boy raises/lowers with the push of a button.
Either mower will give you years of service with proper care. Price, dealer service, comfort, and location of dealer should help you make the choice. Kubota has a great reputation. But in my area Bad Boy has taken over in the homeowner market and a lot of commercial mowers use them. I looked at the manufacturers websites and the Bad Bod cuts 12" more and looks to be a slightly heavier duty machine. By that I mean wider tires, etc..
Don't think you could go wrong with either one.