I think you're one of the few people I've seen complain about the merged layers/objects view... Do you use Inkscape frequently & as an artist, or is it in a different capacity? Is it the principle that annoys you, or just the bugs you mentioned?
I personally welcome the idea a lot, as I don't have to travel 70% of screen distance to swap between layers and objects. In fact, I was using the XML window because of how annoying the old UI was. Also, now its much much easier to organise larger projects into something structured. Previously half the time I would spam send below/above commands on a select object until it popped into place. Now I don't even think about it, it almost just happens because I'm already "in" the place I want my object to be.
I've used and evangelised for inkscape for many years, but I wish I had the skills to contribute to it in a meaningful way for areas like this.