Any word on whether symlinks are an appropriate way to get around editing all those mod.ini files?
A symlink will probably work fine, but the issue is mediavps (the 3.6.10 vps) and mediavps_3612 are separate but mostly compatible mods, which means you may need to be able to use the real 3.6.10 vps if you have issues with a mod.
As mod.ini is read by FSO and its utilities, they could lowercase all folder references. Just sayin'.
To be pedantic, FSO does not read mod.ini (nor does FRED for that matter) only the launchers may.
That being said, it is probably the best option, which IIRC is the same one that FSO internally for finding an asset in the mods folders to attempt to avoid this entire issue.
I read that the new wxLauncher is going to replace it. Is that true? Can I look forward to it in the near future? Will there be ponies? 
There is a new version of Turey's installer that Goober5000 is working on, which will be out fairly soon as Goober already noted. wxLauncher's install capabilities are quite a while off unfortunately. Sorry, you missed the ponies, they were here on April 1st, 2011

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