This is my first time suggesting a new idea - so please be gently :-). And please challenge my idea and add yours as well.
Many people are developing blogs and websites for clients, and different solutions requires different features or functionality. Often existing plugins are used to extend WP.
When developing a new solution/theme, customizing a plugin is required. After the launch of the solution it needs updates to keep up with security and new features.
Customization of a plugin is different from plugin to plugin.
Most of them have no mo/po files, or the possibility to add your own theme style.
Some might offer the solutions to add your own styles within the dashboard. But in different places and often very limited.
The problem occurs when you update your plugin. You might have added div tags, edited the style, and translated labels to your language, that is overwritten when you update.
Having a framework for plugins. A set of standards how a plugin should accept customization, so you can customize and update the plugin in the future without breaking it.
Ian Dunn has suggested a child plugin (http://wordpress.org/extend/ideas/topic/child-plugins). That is a great idea but lets extend and describe that a little bit.
1) mo/po implementation
2) the possibility to add external style sheet
3) the possibility to copy the files to a sub-folder within your theme (like a child theme)
To make the idea fly
a) Consider a compliant logo/name for plugins that follow the standards, and make users decide if the plugin is compliant (like the existing compatibility box).
c) Make it optional for developers if they want to be compliant, so we do not throw away all the existing plugins in wordpress.org/extend.
d) Having a compliant package with a barebone setup and user guide for plugin developers will make it easy for developers to reach the complaints.