I understand the need to keep a default for keyboard shortcuts (helps out new users when following along with training or freelancers on different machines, etc) and I think this proposed solution can work fine.
However as After Effects continues to grow in functionality and complexity, a standard set of keyboard shortcuts is only going to be more and more difficult to add & modify. I know that there are scripts like KeyEd Up to help customize shortcuts but I think ultimately After Effects could focus on a more mature solution in this vein.
Are you familiar with how Final Cut Pro 7's keyboard shortcuts were implemented? They totally nailed it. You had a searchable list of all commands, a visual keyboard of what was currently mapped (with modifiers), and drag and drop assigning. Perfect.
At the very least, steal Premiere's implementation? Either way, there's a limited number of keys and a growing amount of features. All operations in After Effects should be keyboardable, not just a limited set. Sure, start with a universal default set, but I think we'd all get more functionality if we could then completely customize to the way we work. Throw in keyboard presets that closely approximate mappings for Premiere, Photoshop, Cinema4d, etc to help bridge the gap.
Basically, present us with a searchable list of every command, menu item, tool/palette, how they're currently mapped (by default & by modifiers) and the ability to change, import and export those preferences.
[branched from discussion on different subject]