When AA and US merged, there was a bit of a 'crunch' on flight numbers and AA needed to combine some legs in order to have enough flight numbers. At that time, AA chose to make a good number of AAA-BBB-AAA flights as well as increased usage of AAA-BBB-CCC flight numbers (especially adding domestic segments to international flight numbers). Why AA didn't opt for more of the AAA-BBB-CCC variety rather than doing so much AAA-BBB-AAA I can't say. Doesn't seem to harm anything, though it does drive confusions for fliers every once in a while.

As for flight numbers changing, I've noticed this on AA and all the US majors. Every few months a lot of flight numbers will swap out. I've always speculated that that this is intended to reset 'on-time numbers' for the flight but I could be totally off base.

AA and the US majors don't really use consecutive flight numbers in any organized manner like BA does. There are some (non-binding) numbering patterns that have emerged (many ORD-LGA are in the 300s for example) but it's just not something the US majors tend to focus on in general.