Since I spend my time on both locations, the diving in Bali is definitely better but the instruction in Phuket is more structured. Phuket now churns up the most instructors in Asia and I think in the world. It's a livestyle thing, Phuket has the night life (albeit sleazy and less sophisticated), great food and interesting culture, big rainforests and plenty of activities. Bali has a certain mystique, not attached to the mainland and generally a different crowd depending on which town you stay in. The nightlife in Seminyak is legendary and more sophisticated.
I'm assuming you are already above rescue diver etc. going from zero -120 dives for instructor certification is also done around thailand.