I find it strange that my meta webapp and webpp reputation are linked to each other. Don't you think that the ability to discuss meta topics is completely different from the ability to provide good answers to solid questions?
A few reasons... at least this is the current thinking:
The more you participate on webapps, the more "stake" you should have in how the site is governed and run here on meta.
Since votes on meta no longer "hurt" or "harm" for reputation people are more free to cast votes on the content of posts, without worrying about the effect on the poster's rep.
The focus should be on participation on the parent site; participation on meta should never become a rep-generating goal in and of itself.
I plan to blog about this soon, but that's the gist of it.