I was listening to an interesting interview on NPR the other day with this guy who said the twin towers did not make much sense from a city planning point of view. As it was already stated, you could build several smaller buildings for the price of the two towers.
More importantly, these two big buildings concentrated things too much. Aside from the enormous infrastructure needed to support them, it made too many people needing to commute to an already overcrowded place. Getting into Manhattan is a nightmare, and you have to build and maintain a gamut of bridges and tunnels just to provide access. His theory was to spread this space over the NYC area, not just in Manhattan (like the Bronx and Brooklyn, etc. ) to stimulate economic development in these areas, and ease commuting. This would also avoid making one giant, vulnerable target that would be begging to be hit again (even if you kill all the islamic terrorists, the next psychos will go for it) Strategically this makes sense as well.
Personally, I'd like to see the towers again because they were so cool, although we must be careful about creating another giant Acheilles' Heel. It should also be noted that this guys perspective was that the original towers marred the beautiful NY skyline, for whatever that is worth. He had some convincing and insightful points however.