I can appreciate the desired option. It makes sense. As a person who works on a mod and generates lots of test worlds, I'd also appreciate the ability to keep a modlet in one place -- what we currently have. A compromise might be that when you start a world all of the modlets found in your mods folder get copied to the generated world.
Another option -- something I'd hope to see with Steam Workshop Support -- is that when starting a world you selected which mods should be applied to that world via some UI and then the game could find/load those modlets in the mods folder, but would just ignore any modlets that you didn't select for that world. Copying mods around on a system is a waste of space.
Steam Workshop Support I would hope would also allow for automatically downloading updates to mods, plus seamless installation. Those are things that can be confusing and frustrating to users today.