Regarding random reads, keep in mind that most discs are authored based on the title's analyzed usage patterns. Media differences aside, that can give a disc a performance advantage compared to any file copy made from it.
The WiiU FAT implementation is poor. It was made for low volume usage, like saving mii pictures, not running games made of thousands of files. Yes, it's a programming problem. If you can write a better FAT driver, and integrate it with the OS, that would be great.
Loadiine could be changed to natively support FAT instead of using the OS to do it. I think @Billy Acuña was working on that at one point.
Loadiine could also possibly use a scheme of extracing files from a single large file to bypass the file system. The SD itself seems to work respectably when you install games from it, and those usually have large archives in them instead of tons of small files. I don't think anyone will implement an indexed archive approach though. Nobody was interested enough to do it before we had wupinstalled titles.
