I think that all mod loaders should use a mods folder in the minecraft directory selected by the profile.
Both 1.5.2 and 1.6.1 the servers.dat file is the one pointed to by the directory entry in the profile.
Have that directory structure containing all of the data for that profile only make since.
I don't know how many times I have accidentally loaded SSP world with a mod pack I had used for it missing and had blocks and items vanish. It really sucks.
Lex, please think of the not-so-enlightened that build their own packs.
Personally, I would have preferred something like:
/mods/(ForgeVersionName)/ModPack(s).jar
Nice and simple, allows for switching between mods based on the version they use in the minecraft launcher profiles.
Food for thought...
The only reason to have a version under the mods directory would be useful if for some reason you were running different versions in the same directory, but you would still run into the problem of blocks/items not supported in one version or another vanishing. So I think it would be better just to keep them separate and just move the save to the version you wanted to play it on.
Right now I'm just renaming into the libraries directory and adding into the jason file for the version so I can have different versions with different mods, now if I can only figure out how to stop them from trying to update.
In the future it looks like mods will be going in resource packs. See https://gist.github.com/Dinnerbone/5662824
This post contains mostly my opinions and I take full responsibility for the ones that are mine.