In Linux, encrypting user data usually involves just using an encrypted partition/container for the user's /home directory. All user data is stored there so the user is reasonably safe. In Android, all user data is stored on the same partition, the /data partition. The user data for apps goes into /data/user/(userid), the emulated external storage into /data/media. The binary files for apps are shared between users and are located in /data/app and /data/lib. In other words: user data can be all over the place.
Theoretically, you could create a partition for each user's data and emulated external storage, encrypt that and set up the mounting points/symbolic links so that all encryption is done transparently.
However, this would require some serious changes to the file system and probably to the ROM and kernel itself as well because the system must have the /data/user/x directories mounted at boot time. I've never heard of a (custom) ROM that does this, so if you want all your user data to be encrypted you'll have to program it yourself.
If your device has a lot of custom ROMs you might be able to download and modify an existing ROM with some boot scripts. This would probably be a lot of work though.