Oh, I'm another person that command-~ doesn't work for. I mean, it can work, but let's say I am working with three apps - two of them are web apps in their own chrome windows, three more chrome windows that I don't care about at the moment, and Numbers. I need to swap between the two because the monitor isn't big enough to show all the information at the same time.
I have to think about whether I want to tab or tilde at the moment, and then I have to make sure to minimize anything I'm not actively working on (or move it to a different space.)
But if I want something on a different space, then I have to think about moving over there because command-~ won't go there. So, I have to keep context in my mind that I want to Just Work.
I think if I could split out things like gmail, google calendar, or other SAASes rather than being separate windows I'd be better off. (I've created electron apps for some of these in the past, but it does make links out of them messy.)
I have a large screen most of the time, so I can keep the necessary context on the screen, but it becomes a larger problem when I'm on just the laptop screen.