There seems to be a growing number of plugins putting their settings menus in different places, and I think it needs to be addressed before it spreads anymore.
Plugins menu location is currently up to the plugin author, and settings are showing up all over the admin panel, in Settings, Tools, and sometimes Appearance, and the especially naughty ones install themselves in the top-level area.
This is annoying behavior. I don't want more top-level settings, and I don't want to have to hunt for settings for each plugin. Ideally, I think plugin setting should be sent to the Plugins menu, as it makes the most sense. Leave the Settings menu to the stock settings, and make it easy to find all settings related to plugins in the plugins menu.
There are a couple of plugins that attempt to remedy this, but it sure seems like it ought to be built into the WordPress base. Admin Menu Editor is a pretty heavy plugin to run if all you want is to put plugin settings in a proper place. Menu Humility has the right idea, but only pushes them to the bottom, and doesn't work with all plugins.
Make a default location for plugin settings to be stored, and make it enforceable by the user. Even better would be drag and drop menu editing.