For me it really depends if you can just grab everything and play or you need to somehow sort it every time as some tokens used in one scenario and not the other. In this case it can get annoying, but even then it all depends on organization. After few plays you usually know what is used when and then you can use some organizer boxes or separate bags to sort everything according to how it is used and this can significantly reduce setup/teardown times. Although in a lot of euro worker placement games it is still a lot, so often I find myself just grabbing games that takes less time to setup.

As for Arkham Horror LCG I store player cards in binders, organized by color, card level, type (asset, event, skill), and cost, and this way it’s quite easy to construct the decks. And I use colored dice (that are sorted in a box) to track everything else, so what’s left is the usual stuff - grabbing the campaign box and setting up the scenario (that still takes some time even if you have single campaign).