By design, I would argue. And a good decision, too.
To use a facetious example just to illustrate my point: without separate reputations, one could build up a huge reputation on http://apple.stackexchange.com/ and then use that influence over at http://askubuntu.com/ to provide a mediocre answer.
This mediocre answer could then get upvoted to the top by those who do not know a better way purely because of this user's reputation. Meanwhile the perfect answer provided by a newcomer to the SE network may remain hidden in second place.
N.B. I think the "bonus" reputation points that can be transferred are a way of addressing this imbalance while pushing people to use other SE sites at the same time.
Now THAT would break the system.
Edit: I created an account on Cooking, and it gave me the linking bonus everywhere. I guess I hadn't created accounts on any Stack Exchange sites since reaching 200 rep on one of them.
Putting rep aside, I don't even know what all the other development-related SE sites are, let alone can be bothered to monitor them all. This means that there are interesting questions I'll never see because I only visit StackOverflow.
I don't see how people other than complete SE junkies are supposed to stay on top of this site creation and forking extravaganza. Good for them, but I don't have the energy.
If I have demonstrated I'm not a spammer by having a solid score on SO then I should be allowed to post a comment straight away on cooking.
That's the reason for the 100rep liking bonus - it's a grandfather clause
edit: I was asked a question which was perfectly answered by rtg. Should've provided more substance, but I wanted to endorse this as being exactly what I was talking about.
The only major broken part (IMO) of SO is that the SE network is becoming so disjointed and your rep doesn't transfer between sites.