I've had 2 YZ250 with weighted flywheels, 18" rear rims, reworked suspension, WR gearboxes, etc. Not quite a 250X, but similar.
Advantages of the YZ: Lighter, better suspension IF set up properly.
Advantages of 300: More torque = less stalling, electric start, hydraulic clutch.
For me, it's a no contest; 300 all the way, but I like extreme technical. I suppose though for more flowing stuff like GNCC, the YZ will be better.