I participate actively on Christianity.SE, which was just graduated. The meta site rep is always equal to the main site there. I like that because I don't have to worry about a rep pounding on the meta site if I make a bad suggestion.
Conversely, here on MSO, the rep is separate from the SO site. I have made a few bad suggestions and have taken quite a pounding for it (over 25% of my total rep on one post). This makes me hesitant to post things on MSO.
So why is it separate rep on MSO and not on the C.SE site?