"storing the mails in the profile is pretty annoying"
For most users it's the correct default, but it should be modifiable (Outlook .pst can be moved). Many users won't have different partitions, while profiles have automatically correct permissions (you can't access another profile directories unless you're an admin) - people creating folders around rarely set the correct ones. Again, reasonable defaults are OK, as long as power user can modify them. The issues arise when dumbed down applications remove any chance of personalization - and most applications are following this path.