I also think there will likely be THREE lines, Epcot to CBR line, The DHS to CBR line, and the CBR to Pop/Animation. Though another possiblity is that The DHS-CBR-Riviera-Epcot is a single line, and the CBR to Pop is it's own line.
I think in general people are overestimating the traffic issues here. Think about it from the perspective of buses:
Right now, CBR has maybe 4 buses per hour going to Epcot normally (one bus every 15 minutes) at peak times. Each bus holds say 75 people on it. Pop and AoA have the same thing, a bus every 15 minutes. So we are talking 12 buses of people leave these three resorts at peak hours heading to Epcot. That's 900 people per hour leaving those three resorts going to the parks. The capacity for the gondola will likely be on the order of 2,500 people per hour. And there's a good chance that they won't eliminate the buses completely. If Disney is thinking properly, you will have people who are afraid of heights and won't want to ride the Gondola, so there will likely still be some amount of buses that have to run to these parks.
I'm not saying their won't be waits at peak times, especially with AoA and Pop coming to CBR and needing to all load at the same station. I just think the overcrowding of the areas are being overstated by some. I wouldn't be surprised if a 10-15 wait for the gondola occurs at peak times, but that's no different from your 20 minute wait for the bus.