I remember a while ago, Ubuntu used encryptfs for home directories, but it was removed. Weird, because I thought it was a great idea
I’ve been using fscrypt to encrypt my home directory for over a year now and it seems to work fine: https://wiki.archlinux.org/index.php/Fscrypt
I also created eCryptfs, which was Ubuntu's original home directory encryption technology, with lots of additional distro integration work by Dustin Kirkland. Unfortunately I had to make some compromises when going with the stackable model, and that caused some problems.
I took the lessons I learned from that first attempt and created fs-crypt as a sort of atonement. I think I got a lot more right on my second attempt at file-base encryption in Linux. At least, it's good enough to be the technology that now encrypts Android storage.
The problem with Linux supporting stuff forever is that some things really need to be retired once a better solution has come along. However so long as there are eCryptfs users out there, I don't think it's going to ever go away at this point.