I'm not sure how much demand there might be for this, or if its too much of a headache to add in, but the launcher could get a bit of a coolness factor with optional skins. It could be useful with Total Conversion Mods, say to have customized launcher skin... say a B5 theme for TBP. It could either be tied into the mod.ini to select that skin as long as its selected, dropping back to default or user-choice default if no mod-designated skin is selected.
On the topic of FRED launching support, it could benefit from including a button that allows it to quickly inherit mod parameters from the currently selected FS_Open mod selection. It would also be useful if the FRED support also included similar (to FSO options) lists of command line arguments, rather than relying on the user to memorize them.
This has also been mentioned before, and the usual answer is that it is too difficult to implement. On the subject of command line arguments, there are a number of lighting-based arguments that aren't listed in the standard menus, because they require the user to input a value.. ambient_factor is an example. I'm sure many would like to see these arguments in lists, with their default values and a brief summary of their effect on lighting, listed.