Another aspect to this is the ability to get emergency exit/bulkhead seats, which have much more leg room.
I'm very tall, thus I would usually try to check in on line as soon as possible, as this is the only way to stand any chance of getting these seats. Even if you arrive very early at the airport you will find they are gone.
A further factor is that even if you have some kind of "frequent flyer" membership with the airline in question (often a criteria in allocation the "best" seats. becaus eof the group booking JY cannot register this against your name/booking.
Like most people on JY holidays, upgrading is not something I could financially consider, thus the way that JY use group bookings, and don't allow you to book you own flights, would make me seriously consider competitors where such an option is possible.
Stuart