Windowed Scale = 3.0 is the size of the game screen when in windowed mode and that is in the general video settings. What I am talking about is in the core options. Most (not all) cores have extra options specifically available to that core which is in the quick menu when you have that core running.
You can try other video drivers but gl is all around the best driver, it's what I use and I have an Nvidia card.
There is no 1920 x 1080, there will only be multiples of the native resolution of the original hardware so the closest would be the 960 resolution. If you want 16:9 you will have to force it in the general video settings and like you said previously, it looks bad. Though some people really prefer it.
You can turn off integer scaling though and it will get rid of most, if not all of the black bars at the top and bottom of the screen.