No choice in the matter really.... Not just because it is a Yamaha, but because of the purpose each quad was built for... The Raptor was set up for more of a intermediate skilled rider (better suspension, better engine, better overall dynamics, no reverse, blah blah blah) where the TRX is a beginners quad (shaft drive, clutch or clutchless, and SLOOOWWW).
Good luck with your choice.