Here's a quick compilation of things that would help a lot in regards to having and organising a second System directory, taken from the other post:

1. UCC MakeCommandlet - add an optional parameter "<output path>" or similar, that would output the compiled Unreal packages into a custom directory, just like the BatchExportCommandlet (at least the one in UT1) does.
2. UCC MakeCommandlet - add an optional parameter "<input path>" or similar, that would attempt to compile code that is in a custom directory, instead of simply one level higher in the directory tree.
3. UnrealEd - make the "Export all" command in the Actor Class Browser ask you for an output directory.
4. Add support for INI files (other than Unreal.ini/UnrealLinux.ini, as this is where the Paths have to be defined in the first place) in custom directories, presumably using Paths=*.ini.
5. UnrealScript - Have SaveConfig() and StaticSaveConfig() put the INI files into the last INI directory defined by Paths.

well, for now I can say that messing with the ini settings is having a huge potential to mess things up, especially for not very experienced users.

UED's Export All doesn't ask for a directory, that's true, but you can now export specific single packages by selection, which does all I need, because I used Export All in older versions only when I needed the classes of a custom package and not using UCC..

anyway, will see if I find the time for some of these things, but to be honest, I'm tired and currently not motivated to take the risk of new bugs due to a new feature (and I didn't want to implement new features for quite some time now).