The only potential disadvantage I could see is that the buttons and controls on a yoke is spread across both hands, whereas on a traditional Joystick you would have them all within reach of one hand.  I'm thinking of the CH yoke vs. Fighterstick specifically here. If you were to add a seperate throttle you'd get more buttons than you could shake a stick at and probably be more efficient.  
With the single yoke if you needed to access a key that wasn't on the yoke itself you'd potentially have to move your hand to the keyboard and back several times during a fight. 
Then again if you laid out the buttons carefully it may be a non-issue, and I would think the increased comfort would more than make up for it.