In settings you can choose which update you are using:
Rahel, we considered creating scale keys, but if there was already a scale timeline this could cause problems. I suppose for bones that don't have a scale timeline we could create keys. However, the old flip would flip bones using the world axes and the new flip uses the bones' local axes, so I'm not sure it would help much. Sorry! The new flip (negative scale) works a whole lot better and makes more sense, it's worth the trouble in the long run. You could always drop back to 2.1.27 and move to v3 for your next project. BTW, keep your 2.1.27 projects safe (you can always find them in your backup folder), because if you save with v3 it will remove your flip timelines. That way if we add code to create keys, you can make use of it.
About resetting the preferences, that has to happen when certain things change sometimes, sorry. We try not to do it, but sometimes it's unavoidable. You can find your old hotkeys in your Spine backup folder (click the button in Settings).
puzzler, are you running in a VM? What OS?
The menu animation duration was reduced in v3 so it should be less annoying than in v2, but you can disable all interface animations as Pharan has shown.
I should also remind everyone that if you save a project with v3, you cannot open it with an older version anymore. However, you can always open an old project with a newer version of Spine.