I don't know if this exact thing has been up, sorry if it has. But I thought perhaps one could have sort of a local svn of the bundles, with only one "level" of fallback (sorry, I don't speak technical svn). So that when you customise an item in a bundle, it will make a copy of that specific entry, and place it first (or last) of all the items (snippets, languages, commands etc), with a big delimiter between "your" stuff and the bundle default stuff. This could upen up for revert commands, and perhaps even diff commands. Also, if you delete something from the original, it can show up among your things with a big linethrough. Perhaps one should also be able to see what sort of "own" things has been forked off original things, so you can compare with the original. Also, you can add your entirely new items into a logical bundle, and you will see that it is yours entirely and not built off an original.
I hope I've made myself clear on the whole idea, and I hope it's not something that's already come up :)
Andreas