So no, what you want (wp-content/uploads on main site in second and subsequent networks) just is not possible.
That's NOT what I want. Obviously, that's not possible and I'm quite happy with the main site(s) using /wp-content/bogs.dir/x/files/ but what I want is for them to visibly use /files/ on the front end like all other sites. But you probably understood that after the reread?
1. reinstall.
Reinstalling would make the main site use /wp-content/uploads/, or not? I already achieved the same result by just editing the main sites options Upload Path and Fileupload Url and manually copying the files from /blogs.dir/1/files/ to /uploads/ ... I'll have to go through every post to edit the URLs but that will be a lot less work than reinstalling the complete network.
So the question remains, what about those main sites of secondary networks? It seems Fileupload Url is ignored there...
See this?
http://atypicalife.net/blog/2011/03/01/worlds-biggest-igloo/5x8o/
It's a rewritten url for an image, right?
It's on a second network.
Ok, but is it on the second networks MAIN site? If so, then where did I muck up? David Dean, any thoughts on this?
Oh, I can do the same by removing the /wp-content/blogs.id/x from the image url manually (leaving the /files/ in there) on any main site and it would work just fine, but since I'm not the one that's going to be taking care of the content of those other main sites, I'd like to have WP use /files/ by default.
Or try this plugin:
http://wordpress.org/extend/plugins/wp-multi-network/
As far as I can tell, that's basically the same plugin. Or at least a similar (semantic) conversion of Multi-Site Manager the predecessor of Networks for WordPress... So I would be highly surprised if that would change anything.
Maybe I do need your paid plugin then...