Yes, cruising the Yangtze River is still well worth the trip! As a China tourism veteran, I've been to the Yangtze many times, and still sending more clients to Yangtze now.
I will recommend take either three days upstream or downstream between Chongqing and Yichang. Since all the highlights are within this distance. You will have one shore excursion per day, which include the Three Gorges Dam site, lesser Three Gorges, Shibaozhai, etc. Of course, on the cruise, you will sail through the dramatic three gorges. You can still see a lot and with water going up, it's more navigable. However, the final date is 2009. I can help you to choose a cruise line according to your need if you decide to take the Yangtze cruise.
Guilin is another of my favorite place in China! It's the most beautiful place in China! The difference is that Guilin is more land tour, Karst formation with evergreen tropical weather makes it a paradise for leisure travel. The highlight would be Li River Cruise, which is much smaller and shorter than the Yangtze Cruise, only half a day, but is life time of memories!
You can pick whatever suit you the most! You can learn more about Yangtze River from our website: http://www.jiasdreamtours.com/yantzeriver.html
More information about Guilin: http://www.jiasdreamtours.com/guilin.html
If you have any questions, please contact me at: Jia@Jiasdreamtours.com