The start page with its list of interesting questions does a very good job in ordering questions. The custom searches, on the other hand, provide very flexible ways to select questions. I'd be happy if there was some way to integrate these two: Use a custom search to specify which questions to display, and then apply the same algorithm which is used for the start page to decide in what order the results should be displayed.
My idea is that I might make the resulting search a bookmark, and likely use this as my main entry point into SO. As I assume others might use it in the same fashion, it might make sense to somehow store a combination of search and ordering and make that the default homepage for SO. For logged-in users only, of course, as otherwise it would be hard to store that information.