FQM is the exception, not the rule. Very few mods can actually be combined without a lot of work. The game could not possibly be programmed to do this well at all.
[edit]Actually, Proportions makes a number of changes to the quadrant and system files, so you would lose all of those if you use it with FQM. This may not be a problem for you, just pointing it out.
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It takes much longer than a second or two to extract larger archived files so that the game can use them. It also requires more RAM usage to store the temp files when the game is running. Using something like the Babylon 5 Mod, FQM Deluxe or TDM Modpack would make nearly all Users have to wait for a few minutes before they could play each time they load up the game.
Subfolders keep the mods together nicely. How often do you randomly go in and move files around? I don't know anyone that does that.
[ March 14, 2003, 03:30: Message edited by: Imperator Fyron ]