I was pondering whether an implementation where you choose your set of shaders like you do mods or lighting settings would be viable?
In other words, you have default shaders with no anti-aliasing. Then you have shaders with 2x, 4x and 8x AA (is 8x really needed though?). To choose shaders like you do mods, you use -sdr argument like you would use -mod.
Of course, for FSO to detect default shaders without additional arguments, you'd need to decide how to name the default shaders. Then you can use whatever other shaders people provide with -sdr argument.
As for AA implementation in shaders, little googling seems to provide few examples in the first three pages of search results.