I would love to look at the physical (input) pins in real time using Visual Watch. I know I can see the pins when I pause the controller, but visual watch in real time would be incredibly useful. Is this possible?
Sure, this is already supported. You can use the Debug->Windows->Hardware Registers window, locate the appropriate pin status register (see the device datasheet for the exact name) and turn on the live mode for it (lightning bolt icon). You can also flag several similar registers as favorite, so you can quickly view their realtime values without having to locate each one individually.