So would you prefer to patch and update Amiga OS 3.1 yourself for a lean system or would you just go with 3.9?
Alternatively should you be able to manually (in a user friendly way) unselect/disable certain resource hogs. Pop up help and a lot of background functions as an example. If Windows is a GUI based OS why do you need to use the 'run program x' to get at some of the options.
The problem with patches is that they are just patches, not final solutions.
AmigaOS 3.9 can be made as nearly as lean as 3.1 if you know how to manually remove (in an unfriendly way) those extra components. I have managed, as an example, to run AmigaOS 3.9 on a 68000, just by removing some extra stuff. So it depends if you feel fine with the downgrade from 3.9 -> 3.1 functionality.
Well, Windows is bloated, but then it is aimed at the user experience, not at being resource efficient, and its hardware architecture advances with such a speed, they really dont have any obligation to optimize their code.