I think the original Arduino design made a decent compromise between being general purpose while self sufficient at the same time. Sure an extra push button would have been useful for some but it didn't make the cut.
The pin 13 LED is very useful to tell if the board is functional by uploading a blink sketch without having to wire anything else up. So it's a quick checkout for the initial IDE installation and set-up (board and comm# selection correct) for someone just starting out.
Keep in mind the ease of adding either a store bought or DIY proto-shield that can contain any 'extra' component items you want.
Lefty