We have had a T900 for about six years, and we have enjoyed it a lot. During that time we have ridden a couple of more sporty tandems, but decided to stick with our T900. It fits our fun riding style and has been reliable all the way.
Like you mentioned, we switched to 26x1.5 road tires (Schwalbe Marathon Racers). Not only did they knock almost two pounds of rotating mass off of the bike, but they roll easier and actually ride better than the stock tires. They made a BIG difference! (To their credit, the stock tires lasted forever, and they were good dual-purpose tires).
I switched to a more sporty saddle. My wife (the stoker) tried other saddles, but stuck with the stock saddle. It weighs a ton, but it's the most comfortable seat she has tried.
We never had any complaints about the stock brakes, but after cooking them on a very long, steep hill we installed some KoolStops and were blown away by how much better they were.
I think the T900 is the least expensive way to get a really good quality tandem. Work with your wife on communication and trust rules, and you will have a great time enjoying the wind in your face, the great outdoors and a good work out! Have fun!
Suggestions from Sheldon Brown:
http://www.sheldonbrown.com/tandem.html