I have an idea, don't know how feasable it is. I keep seeing requests on how to exclude muliple categories on the main page, as well as controling the order of the category list in the menu.
Here's my suggestions:
1) add a sort number to the category admin page. This would allow users to set a number for each category to control the order they want them to be in. A sort order of 0 would hide the category link on the main page.
2) Add a checkbox that would control if the posts from that category would "Show on Main Page" with a default True. Then if it's unchecked no posts from that category would be shown on the main page.
So, those are my ideas. Take them or leave them, doesn't matter to me.