There are many differences between SM and PU. One is the SM is supposed to have everything in it, a "single stop shop", and PU is only supposed to have things that work for a particular version, and that presumably work together. Of course, SM doesn't have everything, and it is easy to put two packages in PU that do not work together. Reality is never quite up to our expectations. Nevertheless, SM is more "universal" than PU, and a PU is more coherent and the things in it are more likely to work together than SM.
One way to solve this is to make SM more automatic. It could be given rules about where a particular package could be found and could update itself automatically. So, it could get its latest version from a MC repository or from a PU.
Another way is to change PU so that when you update a PU, it automatically updaes SM.
Personally, I prefer the PU model to the SM model, though it is certainly useful to have a complete list of Squeak projects, even if the projects are often out of date and won't run in my current image. Most of the time I prefer to have software that I can assume works.
-Ralph