I havn't had the chance to ride an Apex, so I cant give you a "seat of the pants" opinion about it yet. I have been on a few different RX-1 mountain's, including a couple of turbo charged one's. The turbo's really haul azz! Feel's like the power is never going to quit!
I do perfer my modded Viper over the stock RX-1 Mtn though. For me the Viper is more fun to ride, easier to boondock with, and overall just more agile.
Those who have rode the Apex, say that handle's better then a RX-1. Not that the RX handles badly, it's just different then what I'm used to.
At this point I'll stay with the piped Viper. I really like it, I do a fair amount of drag racing, and it works well for that also. If I was to buy an Apex, I would need to ride one first to see how I like it.
So far no problems with the motor. After 3 season's with pipes, it's still going strong. IMO, some pipes can make the motor more sensitive to burn downs then others. But most problems can be traced to improper jetting or poor fuel quality.