I guess I'd consider myself an "experienced alt-tab user", and I have this frustration on a regular basis. Yes, as you say, I can manually reorder the apps, but it annoys me to have to do so.
Same here. I've solved the problem by not using any of this alt-tab behaviour. I have a suboptimal usage pattern that's still more intuitive than alt-tab.
I've bound alt-tab and ctrl-tab to raise/lower window. While I do use four virtual desktops to group windows of similar interest, I generally just hide the frontmost window when I want to switch. This keeps the cycle static and I can do most things by using keyboard only. I rarely have more than 3-4 windows on a single desktop so I've kind of manually grouped the desired applications together already. If I want to break the cycle and switch directly to a specific window, I just point my mouse to it and use the keyboard to raise it front.
I've bound alt-tab and ctrl-tab to raise/lower window. While I do use four virtual desktops to group windows of similar interest, I generally just hide the frontmost window when I want to switch. This keeps the cycle static and I can do most things by using keyboard only. I rarely have more than 3-4 windows on a single desktop so I've kind of manually grouped the desired applications together already. If I want to break the cycle and switch directly to a specific window, I just point my mouse to it and use the keyboard to raise it front.