There is no doubt that the EQII application deployment architecture is pretty sad. I was reading some forum posts by a user who pointed out that SOE's sloppy decision to store cache and log files in that application directory (and hard-wire those paths) made it nearly impossible to improve performance by installing it on an SSD.
It also doesn't help that the average user is pretty clueless about how their computer works. But that's what we have to work with.
I think re-writing in C++ and publishing through someone like SourceForge is a good idea for the long-term maintainability of the code. And it is an application worth keeping alive for the long haul.