But you can have your cake and eat it, too. Instead of considering the entirety of the updates as forced, why not write/use software that processes each individual update (i.e. per power, item, rule, etc.)?
I don't believe the level of cake I want to have and eat too is something that is practical for the machine. We are now talking about a realm where humans do something better than computers can present it to them.
If I hold up a rulebook, I can say, "we'll be using this book, but we won't include the Frobning class, or feats X, Y, or Z" you'll have very little trouble absorbing that information.
If that interaction is between me and a computer, the computer must present a toggle for every single element that you want to be able to turn on and off. One things computers do poorly is present huge numbers of options in a comprehensible way.
And that doesn't even get us to the point of being able to alter elements ("We'll be using feat Y, but I've changed the prerequisites, and I've nerfed the bonus a bit"), swap elements ("I'm using rangers, but they have powers J, M, and Q instead of A, B, and C") or add entirely new elements or sub-systems, ("Here are firearms, they work in a fundamentally different way than other weapons" or "This system doesn't have action points - here is my action point system").
The complexity required for a machine to allow the above is... well, let's say I think it is a UI and systems problem that won't be conquered any time in the near future.