Waterworks is a fun shortish type course, so I wouldn't miss it if you're in town. I would suggest that with all the great courses that we have in the area that you might think about picking either Swope or Rosedale (I'd go with Swope personally). They're both similar lengths, but I think Swope offers more challenging shots and variety, better scenery and is usually less crowded.
You might consider playing Blue Valley for a real challenge. It's really a world class course with world class difficulty and is sadly usually deserted, save for a few people using the shelters. The course is never crowded. The 3 new courses up in Smithville are a lot of fun as well, playing around the lake, but they might be crowded that weekend. Wyandotte is another really, really great course that often gets overlooked. I really think it's one of the best around, and in a great park but nobody seems to mention it. It's a little bit of drive from where I live up north, but it's much newer, better maintained and more fun than Rosedale (up top), IMO.