With the current design of the settings pages in WordPress, plugins have a very hard time customizing the settings interface, as most panels have only a few specific places where custom code can be inserted via action.
To make this much easier to deal with, the built in settings pages should be reimplemented as a stack of render functions attached to individual actions per section.
These sections should also be attached by actions, so that any plugin can replace or augment a setting on a case by case basis, by simply adding new render functions to the same action, or by replacing the existing render function.
An alternative (more difficult, but I think more valuable) would be to re-implement settings pages to use the custom fields API. This would be a great test of the custom fields API.
Either way, the concept involved gets my vote!