I ride an '02 S3 (bought it brand new) and test rode both the 1050 S3 and the 675 last summer when the Triumph Demo Truck was in town. I also test rode a Thruxton, but that is not applicable to this particular discussion...
The new S3 is nice, but didn't appear to me to be a much different riding experience than my '02. It felt a tiny bit snappier and the throttle response was a tad smoother, but all in all the new look alone didn't make me want to trade in my '02 for a new one.
The 675 was a completely different beast. Aggressive riding posture, ultra flickable and lightweight (like a fighter jet!). The engine just spins effortlessly and has a great howl to it - intoxicating! However, after a 15 minute test ride, my neck, wrists, back, and ankles were sore and I felt very bunched up on it (I'm 6'-3", 190lbs).
I ride my S3 similar to you - long 250-300 mile day trips in the mountains with minimal stops (I've done a couple +500 mile days on it too!) and have been in total comfort.
If you're the sort of person that has to have the new model of everything and are totally in love with the new styling of the S3, then get it. Otherwise, I'd stick with your '02...