Why do they both need separated? There are three peripheral ports, two switches, and a slot, you may as well group them as such. And region should probably be the only thing being hidden.
They may be "ports", but there's a lot of difference between a controller and an expansion port peripheral.
And why show the expansion port setting by default? The BS-X add-on won't affect any non-BSX games, so I don't know why anyone would want to turn it on. And everyone who doesn't know what it is will just be confused by the option.
Keyboard for console games, eh?
It's convenient, and works fine for RPGs, at least.
Well, you probably have a better defense for #3 than #2 then.
Meh. When emulator window does not have focus:
"Allow Input" - you're using a game pad, maybe have the window set to always on top, and want to be able to press buttons regardless of focus.
"Ignore Input" - you're using a keyboard, and don't want IM typing to be sent to the same, but you don't necessarily want to stop the game and music just because you switched a way for a second. More like a real console, where you'd just hit pause and walk away for a bit.
"Pause Emulation" - good for either keyboard or mouse, great for action games and games without a pause feature.
Clutter is an issue, sure. When I have enough other options to justify a miscellaneous panel, I can always move it there.