I would start with just talking with the instructor. Do they seem to be excited about it? Do you think you'll mesh with their personality/teaching style? My girlfriend (ok, I am a little biased) is very excited about teaching, and she wants you to be excited about learning. On the other hand, I have seen instructors that just consider teaching as just part of the job. I think this results in poorer teaching quality.
Next, ask about average class size. Many shops will offer large classes to keep the economics of it more affordable to the student. Yes, this can definitely affect the quality of the instruction based on the instructor and student(s). On the flip side, private classes are available for the one-on-one instruction and attention. You need to decide which works with your schedule and pocketbook.
Also, regarding large classes, do they have qualified assistants in the water? Do the qualified assistants just babysit or do they help with skills? Assistants that actually assist results in more personal training.
What diving has the instructor done outside of instructing? You want an instructor that has credibility. Granted, if you are taking your classes in Bonaire, don't expect your instructor to have Great Lakes' experience. On the flip side, if you are taking classes in Chicago but plan to travel to dive, your instructor will more than likely have Carribean experience.
Be wary of instructors with the minimum number of dives. These instructors may have gone from 0 to 100 during their "road to instructor" class. I have known a handful of instructors that have completed the instructor training, but still need to dive more to get the count higher to receive the instructor rating. As a bare minimum (in my opinion), the instructor should meet the minimum dives with just their fun dives.