Ok, it's a good plan for future mods, but it's a disaster for previously-made stuff.
This still means rearranging your add-ons folder, which means we'll still have the add-ons/add-ons problem, that won't be fixed, and many of us might just drag and drop our entire add-ons folder into add-ons/add-ons or something otherwise stupid. Everyone's add-ons will be broken, and the help section'll get flooded, but that's to be expected.
Since folders would still work, it's not as bad for us coders. In fact, might help us get more organized. A lot of my problems are quelled now, but everyone should still be aware of the upcoming problems. We'll be dealing with them often, looks like, so glar.
And I do intend to port previously-made mods at least, since nobody else would do it probably. Nothing motivates more than being annoyed over something.