It's not difficult to remember like it's some midday/evening after PM rush swap. Weekends and overnight via 63rd, all other times via 53rd. Commuters aren't idiots and will figure it out. Regardless you'll have service to 6th Av one way and QBL the other. They didn't have any issues sending the via the bridge over the weekend back when they were renovating Montague.
Will it involve change and adjustments, something the MTA is allergic to? Yes. But you can fix a backup on one of the busiest trunk lines. Just because it makes things slightly more annoying for operations doesn't mean it won't greatly benefit commuters with fewer delays.
Just look at the overcrowding at Roosevelt that lead to that person falling onto the tracks the other day. 53rd is much busier than 63rd, and right now the is overcrowded, the is slightly less so, and carries air. If we ran twice as many express trains through 53rd you could relieve some congestion on the and crowding at Roosevelt from people passing up and for the . When the was around it carried air despite the MTA's attempts at sending it 53rd to relieve the , and they're still doing the same thing today.