Hi Kristof,
On one side, I would suggest to coregister one by one, as this option is more attractive when you try to do operational works, let’s say you need to coregister a new scene each 6 days. Or when you decide to continue your work by adding one more year of data. On the other side creating giant stacks requires also more powerful computing environments to work.
Depending of the application the selection of master image can matters or not much. For interferometric application it matters, but for amplitude analysis it is not that much relevant. You could select first image as master, and use all the other ones as slave.
This is only my personal point of view, as I said it depends on the desired application.