@FLCA026 The ferries generally are direct, they don't stop at the other resort en route. The flag colour tells you which resort it serves (yellow for Riverside, purple for FQ, and dual yellow/purple if it happens to be a combined service). That said, if a guest asks to be dropped off at FQ, they will happily accommodate them as it takes almost no extra time.
Queues can indeed get quite long - especially late afternoon/early evening, when there can often be a couple of boatfuls of people waiting. There will be more than one boat on the route, but if the line is up to the walkway by the Marina Rentals kiosk, I would suggest getting the bus instead if you are in a hurry, as you could have to wait a while.
We wanted to go from Riverside to FQ at around 7pm one evening, and by then there were a lot of people waiting to go to Disney Springs. Rather than taking up four seats on the main ferry, the captain called for another smaller boat and we were given a private high speed ride, we got there in about two minutes! The driver said he often hangs around the resorts to do this at very busy times, but was a lovely bit of extra magic for us.
Andre