If When Turey's installer becomes mainstream (if it's not that already), there's probably going to be some kind of consistent naming scheme amongst the newbies that install FS2_Open for first time. In that situation, pre-assembled mod.ini files would work just fine.
Those who would want to use more complex mod systems can usually take care of themselves, since they usually have an adequate grasp of FS2 Open mod system and structure. For example, if I play SCP Derelict, my custom mod command line is
-mod Derelict_SCP,mv_beamz_DDS_HIGH,DDS_Beamglows,mediavp368zeta
