I have some experience with both these boats, and they are very hard to compare, as they are both quite unique boats, and vastly different in size.
My best friend bought the Yamaha AR230 two years ago, while I picked up a used Utopia 185, and my sister and her husband have a Challenger 180se as a second boat.
I looked long and hard at both the boats you are interested in at the boat show, and ended up with the used Utopia, because for me the Challenger felt a little cramped, and the Yamaha was to big to fit in my garage. The first thing is the Yamaha dwarfs the little Challenger in size. At 21 feet on the nose, it is 3' 5" longer, and because of the squared off bow seems 5' longer when you sit in the interior. Having used both the Yamaha, and the Sea-Doo on the water, the Yamaha has the most user friendly and well laid out interior and swim platform on the market out of any boat I have ever seen. (remember I still bought a Sea-Doo)
Depending on your location and tow vehicle, the Challenger is much easier to tow and store so keep this in mind.
The Yamaha is quicker out of the hole (twin engine)
The Challenger is a bit better on fuel, and cheaper on maintenance
The Yamaha low speed handling is dismal at best. I can't stress that enough. Below 2000rpm or about five miles an hour the Yamaha's are floating corks.
The Sea-Doo's are the closest thing to a stern drive in handling you will find in a jet boat. (admittedly reverse is a bit weak)
The Yamaha has topside jet clean outs that tend to come in handy.
The Challenger has closed loop cooling.
These are some quick pro's and con's that I have noticed when using both boats, but at the end of the day you should go sit in and crawl around both of them to see which one you feel will work best for your situation. If at all possible, try and arrange an on water test, even if you have to rent the boat.
Good luck, and have fun.
Aaron