Author of eCryptfs and EXT4 encryption chiming in.

"Series of issues?" Really? There were 3, and they were all scored "Low" by the authors for exploitability and security impact.

That said, I generally agree FDE is the way to go if your platform's constraints allow for it -- but only for security. Native EXT4 encryption will give you equal or better performance than FDE primarily because the file system metadata isn't encrypted. Which isn't to say that's a good tradeoff -- it's just the nature of the beast.

Because of performance and functionality issues (file name length, possibility of page cache inconsistency) eCryptfs shouldn't be used for anything any more.