well there wouldn't be any problems if everyone had a clean set of normal looking files, forget about developers they should be creating for the end user (non-developer) the novices will one day inherit the earth didn't you know that ? :))
let's just say for the sake of it, that some might find wp- on every file useful for whatever purpose it may be, they would not represent the majority of end users therefore it would not be justified to have the files that way.
It might be true that some end users don't care, that is until their plugin breaks and it will and they have to go through a boat load of wp-files, personally i don't like the extensions so i purge all folders and files of it and now I can wiz through my search more easily. We all know the real reason wp- is added (so lets not kid anyone :)
If WP took a vote, i'm betting many would prefer just standarized file naming