Originally posted by Bobboau
it sounds bass acwards to me, if you want unmodified FS just don't put any comand line in
If you never use FRED there's no reason not to do it that way
If you do FRED however you have to move the Data folder from the -mod folder every time you want to work in FRED. You then have to move it back every time you want to play any campaign other than the one you're currently working on (because even with the mod switch active Freespace still looks in Freespace2\Data).
Creating a data folder for the main Freespace2 Campaign won't prevent any of that but what it does do is prevent you from having to drag
that folder around as well (or continuously rename it).
What makes it an even more sensible idea to create an Unmodified_FS2 folder is that the second you decide to work on a mod you'll find that you need to put the original data folder somewhere anyway so you might as well do what I said and save yourself some hassle

Of course this entire issue will go away once FRED has a -mod switch.
The other advantage is that you can turn it into a Modified_Main_Campaign folder if you decide to add things like Lightspeed's weapon upgrades. Do that with the main Data folder and you're risking serious problems later down the line.