Bit late to this thread, sorry, but I wanted to say that this is just another example of lowest common denominator programming.
It looks like an improvement, because cosmetically it looks more 'modern', but in reality it's less functional and more frustrating to use than the old program. That's mainly because it's just a straight port from the iPad, so of course it's less functional on MacOS. The main problem is the lack of keyboard features — there's no way of getting at some features with the keyboard, and there's no way of discovering the few shortcuts which have survived from the previous version. E.g. The old shortcut to get the notes panel services, but you can't get to the contents panel with the keyboard; you can bring up the search panel with a shortcut, but once you're there, you have to use the mouse to scroll through the list and so on.
Worse, some of the shortcuts that do survive (e.g. Left and right arrows) randomly stop working when you're in one of the panels. It's a complete mess and it's clear that little if any thought has been put into fitting the app to the OS. (Actually, you get the same frustrating friction using the iPad app with an external keyboard, but at least there it's a bit more understandable.)
Finally, it seems that the program has stopped catering for Mac URL links (kindle://) so programs like Hookmark can no longer link to locations.
I understand the reasons why they think this is the way forward (only one codebase to maintain) but that doesn't mean it benefits users. I don't know how long the old version will keep working, but until it stops, it's probably better not to downgrade to the new one just yet.