The two subs were designed for different mission capabilities.  The seawolf subs are the best in the world at sub on ship or sub on sub combat, as the primary mission for these badboys was taking on russian ballistic missile sub groups (at that time the russian navy would have one or more advanced attack subs "guard" the boomer, which made sucessfull attack by western subs much more difficult, and probably a near suicide mission, success or not, and seawolf was meant to change that ).  the virgina class has the most flexible mission capability criteria of any attack sub by far, making it the best sub out there for most missions that US subs undertake, as subhunting and anti-shipping are but a few of the USN sub forces' jobs.  As they are still superb fighting ships and are more flexible, they are considered the most advanced subs.

   It is still a shame we didnt build more seawolf subs though.

The virginia is longer, I thought ops in shallow water was harder with longer boats?