The new shortcuts pane wastes vertical space and the reload button is in the wrong place (à la Firefox).
I prefer to use the tree view in the shortcuts pane so it doesn't waste space. I use pathbar style, so the reload button thing doesn't concern me, though I can see why it might annoy some people.
As for gtk3 theming, I prefer dark themes (white text on black), and the closest thing I've found is a theme called xfce-dusk-gtk3, but it hasn't been updated in a year. gtk3 theming standards have changed a bit since then, so I get some visual anomalies and a bunch of warnings in the terminal.
What do you mean by native graphics system? Why has it been removed?
Qt4 supports 3 graphics systems (backends): native, raster, opengl
which can be changed when application is started.
Qt5 supports only raster. Native was probably removed because it isn't platform independent and they don't want to fix Linux specific bugs.