Sorry to hear that...
The short ratio transmission was built for acceleration, not stop and go traffic. It sucks sometimes but if I cared that much, I would be driving a Civic or Accord right now. You need your car for different reasons than I do, so it is understandable that you don't like the gear ratios.
You could try a different transmission. I couldn't tell you off hand which would fit your car but that could be a shot. Could be a bad transmission you have now.
If you insist on having an automatic for commuting, that is totally understandable because my commutes are anything but easy. Get some other opinions before you decide on this though, since my opinion usually sucks.