@HalloweenWeed, you are probably right, at current state the best choice seems to be not to use AI Suite, which is unfortunate. I would actually enjoy this software if everything would be working as expected. I like the fan profile curve and voltage adjustments from OS, but unfortunately there are too many bugs to enjoy the AI Suite at this time.
@Nodens, I did that at first and I went through registry cleaning leftovers, uninstalled services via 'sc delete ...' and removed related files from HDD. Somehow even after such extensive manual cleanup the installer does not behave in the same way as installing on fresh OS.
When installing on fresh OS for the very first time it works. I saw it install a USB 3 Boost Driver in c:\Program Files, puts all files for the actual Boost utility in c:\Program Files(x86)\Asus\AI Suite\USB 3.0 Boost directory, and added 1 startup entry into registry for the app.
After manual cleanup of pretty much every piece possible, it installs only the actual files into Program Files(x86)\ASUS\AI Suite\..Boost.. directory, but it no longer installs the actual USB 3 Boost Driver in just "Program Files" like before, and it no loner adds the startup entry. I even tried to manually add the startup entry and manually install that Boost Driver. It all results in utility showing "No USB Device" in all subsequent installs and it cannot see my USB 3.0 jump drive, but on the very first install in fresh OS it does show my drive there and I can enable the actual boost for that flash drive.
Also, after install/manual uninstall I saw 4 "USB Root Hub" devices with exclamation points showing up in the device manager that I could not get rid of even with uninstalling them and checking "Delete driver and software", but maybe this is due to me trying to manually install the actual Boost driver manually (I think it was either error 19 or 29).
Basically after a dozen of Windows reinstalls and experiments I came to a conclusion that it is impossible to make USB 3 Boost utility work once an uninstall is attempted. It seems like even after a deep manual cleaning the OS state is still not the same as before the installation of the USB 3 Boost. I don't know, maybe I missed something while manually hunting all pieces in the registry, but I tried it many times.
Nevertheless it is very unfortunately that this is going on and software doesn't work as intended. I still hope that someone can contact the ASUS engineers and maybe they will be able to fix the installer.