Why did Wizards of the Coast change the minimum deck size for Constructed from 40 to 60 cards?
Mark Rosewater wrote a very interesting article a while back called, "20 things that were going to kill Magic the Gathering."

This is the first thing that was going to kill magic at the time.  Here's all he states in that article, but it's the best I can find to answer your question:


  R&amp;D realized that the rules were a problem, so they introduced two
  changes. First, the minimum for Constructed decks was changed from
  forty to sixty. It remained at forty for Limited formats. Second,
  every card but basic lands was limited to no more than four copies.
  Four was chosen because it allowed some consistency for deck building
  but wasn't too much to ensure that the card would always be drawn
  every game.


The second item that was going to kill magic, was the addition of the banned/restricted list.  The first line of that discussion reads:


  The four-of card limits and the increase in deck size helped, but it
  didn't stop the degeneracy...


So, it's pretty clear, that 60 was introduced to limit the "degeneracy" of decks.  If you've ever tried to take your favorite 60 card deck, and squeeze it down to 40 cards, you realize that it's significantly faster at 40 than at 60.