Depends on what you are looking for.
Performance: definitely the Lightning. My grandma's with a 4 lb lower, intake, exhaust, and tune is probably close to as fast as my supercharged Mustang. They are very, very fast, and have tons of cheap potential. It also handles better than the Stang stock for stock.
Comfort: I gotta go with the Lightning again. The interiors are very nice; they ride like a Cadillac compared to the Stang, and are smooth and quiet. Only disadvantage is number of people that can ride.
Economy: Easy. The Stang hands down. The Lightning gets 15 mpg on a good day, where as my car gets 25 on a bad day. Pretty easy choice there.
Now all of this would depend on what shape and condition either of the vehicles are in. I would never get rid of a SN95 in good condition in order to buy a Lightning in bad condition, and vice-versa.