Re: plugins and the admin area, WP handles this question quite well (IMO). Your plugins appear in the plugins page (where you add new ones, disable/delete old ones, etc), then to modify settings they add their own submenu to the admin menu structure, or they add a single link inside an existing common submenu item (in WP-Admin>Tools, usually), or at a minimum they have a settings link in the plugins page.
Something akin would be good; either the plugin makes a "submenu" in the admin page (big plugins would benefit from this, WD for instance) or they add a single settings link to a common submenu.
Um, yes... I already accounted for all of this.
There's no enforcement of plugins having their settings anywhere. Some plugins don't have settings pages if they don't need them, which is cool.
Some plugins need only a single option or a few options as part of a page, some need massive areas. By not putting any rules in place (and thus no programming interface for it), plugins are free to create what they need and nothing more or less than that.
Plugins can, optionally, declare what URL should be used for settings, so that there is a settings link in the main plugin listing. (The very earliest screenshots of the plugin manager, even when it was called the add-on manager, actually showed this!)
Assuming authors do their job properly - and they should, because it makes their life easier - it's consistent and approachable.
The problem is bundled plugins, and WP has this exact problem. It has two plugins bundled with it but unless you knew they were there from past experience, or actually went into the plugins area, you'd never know they were even bundled with it.
Which means if we added big ticket features as part of the base package, you'd still never know they were there unless either we redirected you there after installation, or made it more prominent by auto pushing items to the main admin page even when the plugins weren't installed... either way that means writing special rules and special logic just for those cases.