Let’s think about UI first.
Whilst there are ways to smooth data reads from analog, there will likely always be points “in between” two values, and it doesn’t sound like jittering between two sets of USB inputs is a good thing to be doing. So whilst you could use a library like ResponsiveAnalogRead to smooth out that input (I like it a lot, beats implementing it by hand all the time), you don’t really address the real problem.
An encoder might make more sense, because it’s a digital input: usually emitting Gray code, you can decode it to basically get “left one click/right one click” type data. But: encoders can be mechanically funky, they’re always harder to work with than you think, and they can still have bounce.
Have you considered something like a pair of up/down toggle buttons? Can be small, means you absolutely, positively, won’t swap inputs unless you want to. You just need one digital pin per input, debounce them, and then maybe use some LEDs as indicators. If you think you’re running out of pins, you’re really not - a LED driver chip or GPIO expander will help here. You might be able to get away with one button for ‘cycle’.
In term of ‘suited’ to controller a microcontroller - there’s not really an answer. You need analog inputs for a pot (which most MCUs do), wheras an encoder is digital. I think the question really is: are you asking it to do an analog thing? And I don’t think you are, so I’m not sure the pot is a good idea. Really, you’re doing digital switching, so some kind of digital input - be it a button or encoder - is probably the right answer. I’d lean towards buttons, frankly.
Regarding the rest of the pile: something like a 4052 is a smart idea. However, it’s a fairly old (CMOS) part, and you might want to test it behaves itself with USB data if you haven’t already. It looks like it should work from what I can make out on the datasheet, but I’m not an expert there, and I don’t know if it’ll interfere with the USB data in any way).
Does that help?
(I’d also note there’s a way of doing this pretty much without an MCU, involving a handful of CMOS parts (counters, mainly) and doing analog switch debouncing).