I understand segregating reputation on the different sites, but since meta.SO is being used for discussion of SU and SF as well, it seems prudent for reputation earned on those sites to apply to meta.SO.
While I'm tempted to agree with you, I think there may be more value in the system as is. High rep users on meta are (at least in theory) people who have provided helpful answers and participated meaninfully in discussions. As such, they are probably the best people to have the powers that come with high rep.
Makes more sense to me that if someone wants to bring rep on the other sites into consideration on Meta that they can just view that person's profile and click the Accounts tab to see the rep on the other sites. I don't think it necessarily follows that someone who can answer "how do I do this in C#", or "what's wrong with my freaking server" would also have the right gauge on how the sites should work.