I know some people want to know if the pedi has a sick waiting room and a well waiting room. Also, can you take your preemies back to a room right away, especially in the germy seasons. I know that nutrition/weight gain are usually a main focus, so ask whether or not the amount of their feeds is appropriate? do they need regular weigh-ins? special preemie formula? Also ask about whether or not they will need Synagis shots to keep RSV away.
I found that at our first appointment, the pedi gave us most of the info. we would need to know. Which was great since we had no clue what to ask and I hadn't discovered the preemie board yet.
After the first appointment, we would write down questions as they came up and then take the list to our next appointment (assuming it wasn't an urgent matter).
I agree with the waiting issue. We don't have a separate room, but we get the first appointment of the day and never on a Monday (since that is usually a 'sick child' day). Ask if your pedi has a lot of experience with preemies, and how often you can come in (we initially went weekly for weight checks).
My girls didn't have any lingering health issues other than reflux, so we didn't have to worry about additional GI doctors, pulmonary docs, neuro people, etc. But if your little one has outstanding health complications, I would chat about those as well.