I prefer training in Gi, I love the full arsenal of attacks with the Gi.... However if I'm getting guys ready for a no gi competition or MMA fight, we train no gi.
I feel that limiting yourself in any aspect of grappling will ultimately hurt your overall development. I've seen phenomenal no gi grapplers who are ranked black belts get caught in a gi choke by blue belts because they have no awareness of the attack. I've seen awesome black belts get caught in leg attacks because they never practice defending them, because they only train and learn by IBJJF rules. I've seen great BJJ guys get smashed in MMA because they approach the fight like a grappling match and forget to account for punches. My point is, after 16 years of doing this, I advise to train in all aspects of grappling.