The Times' article points out that with the advent of the Metrocard, the MTA has more accurate data on where passengers are going, and a combination of using that information and polling passengers on modified lines (like the Q) over the 17 years of construction have directed the transit agency to make the subway changes for the better. Even the Straphangers are positive: Gene Russianoff says, "This is a major step forward. It should mean shorter waits, less crowding and more options for hundreds of thousands of riders."
Here's a map (PDF) to get you acquainted with the changes. Noted subway rider Mayor Bloomberg and other city officials will be taking the innaugural ride over the Manhattan Bridge this morning.