Yes, dependencies are necessary IMO. There are many reasons to support packages depending on or extending other packages, just think at portal mods or other big mods (or library-type mods) which may already have their own extensions but currently are mostly handling them occasionally on their sites. A tag <depends> on package manager will make sure they're supported properly in core SMF. Without issues for users who may want to install a package that depends on another one. (and their forum may not have the dependency installed etc).
The same goes (but I don't know if for 2.1) for clashes. (specify when a package conflicts with another).
As for previous versions of a package... Well. Package manager has the upgrade tag, to be used by modders when they create an updated package. It allows to not
require the user all the time to uninstall the previous version of the mod. Instead users can install the update and be done... I'm not sure why this feature isn't more used... To my knowledge it is very (very!) rarely used. Maybe it's because it implies additional work for modders, but I wonder if there is something else, in the design of the tag maybe, or documentation on it, that is missing. Or whatever else could SMF do, to ease the process.