When you start to blur the lines between plugins and themes - it gets that much harder to manage. Child-themes are starting to grow as a viable solution for maintenance / upgrade support on one side, but now the other shoe drops.

I think a better model could be gleaned from the Maintenance Mode plugin (http://wordpress.org/extend/plugins/maintenance-mode/) which used to suffer from the same "overwrite at update" issue. In the latest versions, it looks for a 503.php file in the current theme directory and uses that. If not, it defaults to the standard files from the plugin.

So for plugin css styling - you could either look to the current active theme for a [pluginname].css or to reduce the volume of css files req'd have a plugin.css that all plugins look for. This would also improve the upgrade path where you lose customizations b/c they were stored inside the plugin files. You could copy any meaningful styles from the plugin directory css into your "plugins.css".