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To some extent reputation on an SE site X correlates with your knowledge of the specific subject matter of X - but some large fraction of it correlates with your knowledge of how to use and contribute to any SE site in general.
If you agree that this is true, than you should agree that some percentage of reputation gained on one SE site should contribute to your reputation on all sites.
As a concrete suggestion say 10%.
As Martijn Pieters comment suggests, this already happens in the form of an association bonus.
The feature is intended for experienced users who have already reached this threshold, and are now proceeding to new sites in the network.
That way they aren't "noobs" on the new site, they have 101 rep and can use all the core functions. ...
This "association bonus" is also mentioned in the FAQ -
If you are an experienced Stack Exchange network user with 200 or more reputation on at least one site, you will receive a starting +100 reputation bonus to get you past basic new user restrictions. This will happen automatically on all current Stack Exchange sites where you have an account, and on any other Stack Exchange sites at the time you log in.
To sum things up, as you can see - once you have a certain amount of reputation on one site you are no longer considered a newbie and are awarded 100 rep to bypass all of the newbie limitations like commenting everywhere and down/upvoting. Together with this it should be noted that your expertise in one area does not make you any more competent in another. I am pretty good with programming, hence my 6K+ rep on Stack Overflow. However, I don't have a clue when it comes to apple software, physics, bicycles, wordpress... the list goes on but I'll stop here :P On those sites I am no longer bound by the limitations enforced on new users but my 6K rep means nothing outside of Stack Overflow...
