I didn't run into any issues. And I enjoyed that at most parks the AoA bus stop was located right next to the Pop bus stop, so it's easy to sit back and just grab a bus (or skip a crowded one and snag the less crowded option). The walk from AoA to Pop is very quick, and the resorts do not share busses.
We had a great time departing through AoA and snagging something at their food court, which has a lot of unique options that Pop doesn't have, and when coming back home, we took the time to wander around AoA checking out the themed areas...though, that was mostly the Cars area per my kids request!
Bus times also influenced my choice to stay at Pop, as I did CBR the previous two trips. As far as bus times, I think Pop, with the addition of the AoA line, has the best bus options on the property.