Until we have a purpose-built construct to organize simple feature classes using a folder structure, consider displaying a warning when creating a new Feature Dataset (FD). Something communicating that FDs are used primarily to group spatially integrated Feature Classes (FC). You could also mention the potential overhead incurred with FDs--e.g. every time you open a single FC in a FD for editing, *all* FCs are touched / locked (?). This generates more SQL and could be a performance issue if too many FCs are stored in the same FD.
Sure, pop-ups are annoying and oft-ignored. But it's way to start socialize the primary intended use of FDs. Even better would be to combine a warning with the already requested idea for a folder structure to organize simple FCs by theme, etc.
The 2010 edition of Modeling Our World (nice work; recommended reading) pg 64, mentions two other uses for FDs:
* A) Organizing data access based on database privileges
* B) Organizing FCs for data sharing
This complicates matters slightly by saying for B that:
"... people might use FDs to organize collections of simple feature classes for sharing with others."
Some may get the wrong idea all over again about using FDs as a way to organize data thematically, This makes an even stronger case to implement a new structure in the GDB to organize thematically-related simple FCs. Customers have clearly wanted the latter based on how FDs actually get used (improperly).
People also keep asking to allow FDs to have non-uniform privileges. Of course this also goes against the intended use of FDs. That all FCs in a FD must have the same privileges simply supports the workflow of needing to edit >1 FCs in a FD, directly or indirectly in the same edit session, due to things like topology.
I'm completely onboard with using FDs as they were intended. But it would be helpful to provide a modeling option that satisfies a presently unmet need once you tell people, "Hey, don't use FDs to thematically organize simple FCs." Until then, users will likely continue to "overload" FDs, literally and figuratively.