And how about adding a built-in enable/disable system for mods? This will help also when getting errors that cause serious problems to the forum; if SMF notices that something doens't work properly, automatically (or prompting an advice that invites to) disables that mod (like wordpress, that imho has one of the best plugins system)! 
Don't know if it would be too difficult to add, maybe for the next major release... 
The mod system is not the same with a plugin system. They both serve the same purpose: extending the functionality of a base software, but do it differently.
As said above, you can't really disable mods (unless the mod itself is written to provide some way, but then it's nonstandard anyway), as long as they are exactly that: mods, that is
direct modifications of code. If they were
separate components as far as implementation is concerned, that would be possible.
However, switching SMF to a modular design at that scale (
and switching mods to a different kind of extensions) is unlikely to happen any time soon (meaning years, if ever). In a sense, as explained by Nao, it's a different way of writing the software to be extensible. One way consists in allowing direct modifications of the code itself (mods), and being optimized for it, while the other consists in plugging in various external extensions. (plugins, or whatnot)
SMF is, and for all I can tell, will most likely continue to be, a medium sized piece of software which can be extended by
modifications to get the wanted result with minimum hassles. It has a certain degree of modularity (by its template subsystem and a few others) and it is still small enough for a fair part of it to be fully understood, thus allowing easy modification.
We might see higher degrees of modularity of SMF in the future indeed, as the software grows, but personally, I highly doubt they will consist in implementing a totally different concept of its packages system. (rather, it's continually being improved and will most likely continue to be).
