Lets say I want a mod that isnt compatible with another mod i have? You should make it so that we can make some mods inactive or remove them, though I would prefer making them inactive. Like if you have The Legend Of Notch: Reincarnation and you want the FTB modpack? make the mods that are incompatible in TLoN inactive so you can have FTB without mc Crashing and Breaking down!

There is actually a way to disable mods in a config file before launcher. But there is nothing we can do during runtime.

What I suggest you do is use the new luancher and create profiles for each mod set you wish to use. Setting the profile's gameDir option will allow you to change where the mods folder is and allow you to have compleetly different mod sets.