I will relate my experiences. I did my first jump, also a tandem, at a small DZ (California City). I too really enjoyed the atmosphere of the small DZ. I did my AFF at Perris, mainly because it was a lot closer to where I live.
The biggest advantage I see for using a large DZ is that you can just show up and get trained - they always have plenty of instructors on hand. I imagine small DZs might have restrictions on what days you can get trained, etc. Maybe not, but I would check first to be safe.
I don't know about other large DZs, but I have found Perris to be quite enjoyable. The instructors are a lot of fun to work with, and even though it is a busy school, I have been able to get quality one-on-one time from their instructors, even when I'm not taking a class.
One thing I did that I would recommend against is switching DZs in the middle of AFF. I started at Perris, then did a couple jumps at Elsinore, then finished up at Perris. Each school has its own way of doing things, and I had to repeat some levels because I was switching back and forth. So unless you have any real problems with your AFF instructors, I recommend sticking to one DZ.
These are just some rambling thoughts off the top of my head. Hope it helps.
-- Ei nirobh akashe aka porchi