I believe main difference is that now there's technology to capture Pokemon and people themselves can use Pokemon to defend them from wild ones.I think Hisuian Zorua might just be cuter than regular Zorua. Also, it's so weird to think about how back then Zoroark and Zorua were monsters to be killed due to their illusions being seen as a threat, but in the modern Pokemon world they're seen as unnerving but ultimately harmless as long as you don't provoke them at worst and good companions at best.
Tree branches ruin everything.
No, this is explained in the synopsis for the series:I'm team 'Meh', but if it's twelve more minutes I'm willing to look regardless.. because it does look beautiful.
I'm a bit unsure of the timeline. The teen'ish/guy on the ship at the beginning is the dad at a younger age right? And when he shows the box to the Ginkgo-merchant he confirms he has come to Hisui for a while now?