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Most of the Egit UI components does harm the Eclipse UI guidelines [1]. Especially the Staging view. The problems are not big, mostly it's spacing ;) I think that a team provider is such an important component that it should integrate itself well into the rest of the IDE. [1] http://www.eclipse.org/articles/Article-UI-Guidelines/Contents.html
It takes time to learn UI guidelines, so anyone who has not spent a *lot* of time designing Eclipse UI's will miss stuff. It would be much easier if you could be specific about the issues you have noticed. Opening an issue on the Staging view pointing out the issues will get them resolved and probably some others too. UI issues may appear differently on different platforms, so the developers may not even see what you see, It's good to get a reminder that such a document exists. I added a section on coding conventions and user interface guidelines to the contributor's guide in the wiki.
No specifics