After watching the video about the making of Arduino, it seemed to me that the developers were trying to make something that could be used in schools/universities, which was cheaper than the other evaluation boards around (which were around $100). Remember if you have to buy 100 of them to outfit a classroom, the difference between $100 each and $30 each becomes quite large. It might be the difference between having your proposal to teach microprocessors rejected, rather than accepted.
Also, in practice, whatever you put on the board, either probably won't be needed, or there won't be enough of them. Put on one potentiometer? Someone will need two. Put on a 4-digit LED? Someone will need 6. Or none.
The idea of making a pretty "bare" board with provision for shields to plug in, seems to me to allow for expansion in all sorts of directions. Plus you can just run patch cables to a breadboard if you don't have the right shield to hand.