It's understandable why they gave preference to the people with reservations: the reservations are only good for one day. They had to insure that they could process all of the reservations. It wouldn't be good to have to tell people with reservations "sorry" at closing time just because they didn't have time to process everyone's orders!
I arrived at San Diego Fashion Valley around 11:00. Both lines were LONG. I reasoned that it would be better to come back at 7 or 8, an hour or two before the mall closing at 9, but didn't want to take the chance, and waited in line for 4 hours. Indeed, when I left, the reserved line was MUCH shorter - probably down to a 1-2 hour wait. Probably would have been 15 minutes near closing time.
The main reason seems to have been limited personnel processing orders. Honestly, there were more Apple employees outside tending the line and passing our ice cream, etc. than there were inside processing orders. I think there probably were only 2 to 5 employees handling iPhone orders. The rest of the store was filled with smiling, chatting employees answering the usual questions. You could have walked in and bought a Mac in 10 minutes, no problem.
An employee would come to the door, fetch the next person in line, walk across the store and invite the customer to sit down in a seating area. (My experience was a bit comical, as I was put in the child seating area. I sat down on a very low ball-shaped chair-thing, without realizing that it actually did have a flat bottom to keep it from rolling around. The last person had left it sitting on the round part. When the employee said "please take a seat" I said "OK, I'll try...") Then they'd ask which phone you wanted, went and got it, THEN got your particulars and credit card, then went in the back AGAIN to process the credit card. Then they marched you over to an activation station.
Now, all nice and friendly and personalized. And completely ridiculous. They could have easily cut out all the walking around (I guess it's part of the employee health program) and cut the time in half or more.