I lack the time before bedtime to research answers to all of them. I'll answer some.
I have just merged an update into master for items 1 and 8.
Confirmed that 1 (ability to set Ctrl+R hotkey) is fixed. The behavior on 8 (frame advance should act as Run in debugger) appears different. I plan to let you know in more detail when I have a chance.
For item 2, can you describe in more detail what confused you about the gamepad config window. I have it setup when you can save different mapping profiles for various input devices.
I plan to give steps to reproduce when I have a chance.
For item 3, can you tell me how much CPU fceux is using when you are running the emulator with a loaded ROM? Use top command.
Somehow it stopped affecting me tonight even before I rebuilt it. It may be affected by something else in the environment. I plan to let you know when it affects me again.
For item 4, I'm trying not to hard code widget pixel sizes into the GUI since it I want it to try to auto scale to the resolution of the screen. But I will try to see what I can do about make the window more compact. One thing that I could do is put the entire window in a scrollable viewport so that it can be further shrunk down. But this would only really be valuable if you don't care to see the entire window all the time.
I could take another look at the new debugger window and find if smaller parts of it can be scrolled. I plan to let you know in more detail when I have a chance.
For item 5, is this the NTSC 2x special scaler that is mentioned on the website help pages?
For item 6, do you just need an input device select window like the windows GUI has?
For item 7, I wonder if bringing back the x2,x3, and x4 video prescalers would help with the hardware accel linear filtering? I can look into this.
Yes. I had been using Prescale 2x when not using NTSC 2x.