As a KC native here is my biased opinion
1. Water Works- has elevation, some challenge, and really great views of the city.
2. Blue Valley- yes it is rather long, but I enjoy the heck out of it. It has character, beauty, and poses a significant challenge.
3. Smithville complex (woodhenge and blackthorn...not beaver) I love these two courses and never regret my trip up north to play them. Beauty, challenge, woods, open, long, short...it has it all.
4. Bad Rock Creek- one of the newer courses in town and it has a high fun factor. It's a slightly better version of Lakeside (#8)
5. Wilbur Young- wooded, fun, technical, short-ish but not too short. I really like the challenge of the tight fairways here.
6. Cliff Drive- some really great holes, however there are a few throw away holes that knock this course down a notch or two for me personally. It has some uniqueness not found at most other courses in town.
7. Lakeside in Olathe- this is just a solid respectable course. Nothing will "WOW" you, however you will get a decent challenge and a little bit of exercise.
8. Longview in Ozawkie Ks. about 45 minutes west of Downtown but it has the most unique topography of any course in our area. If you want a small road trip out of town this course has a high fun factor, a little challenge, and some of the best scenery. I really like this course but it's location means I only play it 3 or 4 times a year.
There is a long list of other great courses that are certainly ok but just don't make my top 8 list. Shawnee Mission, WyCo, Rosedale, Swope (I know, you hear people talk about this course, but unless it's set up in the GOLD configuration I find it a very normal course. Good mind you, but nothing amazing). Legacy in Lee's Summit also make the pretty good but not top 8 list.
Hope this helps. Enjoy your time here, we love our disc golf and we count ourselves pretty lucky to be surrounded by some really great courses.