Some background: in the beginning there were only three sites: Stack Overflow, Server Fault and Super User (aka the trilogy sites) where Stack Overflow was naturally the main site of the three so its Meta site got the most attention.
The "combined" http://stackexchange.com/ site still did not exist (as far as I know, would be glad to stand corrected) and it took years for the network to expand and for new sites to appear, while this Meta used to detect bugs, suggest new features and discuss stuff related to the whole network during the whole time.
When http://stackexchange.com/ did appear, its main goal as far as I can see was to act as a portal to all the sites. As Jeff said here, it did have its own Meta but not for the same purpose as other meta sites.
Anyhow looks like https://meta.stackexchange.com/ will be resurrected soon and this historical inconsistency will be remedied. :)