I'm just trying to find out how far we can go without modifying standard packages.
The NetworkManager is a very bad example and often used to point out how messed up Ubuntu is. I hate it, too, and it's the first thing is deinstall on a fresh installation. It's not essential.
However, there are a lot of other packages I can and do remove from the stock desktop distribution without losing much functionality.
For this I do not have to modify any package, but, in the worst case, disable same startup scripts.
So it's more a matter of selecting the right set package for a particular purpose (e.g., Ubuntu desktop vs. server vs. netbook edition) than adapting the packages themselves.
Even if some package is not modular enough for our purpose, I think we could easily
convince the maintainer to split it up into subpackages.