Rom deletion issue is known and confirmed and on our bugtracker.
The blanker issue is known and there is a workaround above. We will sort that in a future image – it’s an underlying OS issue.
Boot time is down to the OS, it’s quite possible Jessie boots slower – not a RetroPie issue though.
Exiting emulatiomstation is actually a bugfix. Before no metadata was saved on exit – so data could be lost. Now it is, and meta data is always saved. Before it was saved if using quit, but not saved is doing shutdown / restart so we tried to make it more consistent. Unfortunately it does take a while to save if you have a lot of roms.