We LOVE Deanna Rose and would highly recommend it! If you are staying downtown then it is a far drive, but possibly still worth it. If you do all the things and look at everything it will easily take you most of the morning and afternoon. You can eat lunch, get ice cream, ride ponies, fish, etc. It's way fun! It is free to enter M-Th but is still worth the $2 admission for the weekend. The other things do cost money, but not a lot and still worth it for a vacation I think.
Crown Center is fun. There is a fun toy store and we also love the free exhibits as someone else mentioned. Plus there is a little candy store right by its and we love to get some candy when we go. There is also Fritz's where the food gets delivered by a train. You can easily be entertained for a few hours. Across the street there is a fountain that you can run through, just be sure to bring extra clothes, but the kids will love it. And yes, Kaliedoscope is great!
Westport is not all that kid friendly, but there is an amazing ice cream place called Murray's and it's only a 10 minute drive from downtown. It's a local place and they make all their ice cream in store. It's honestly the best ice cream I've ever had and I highly recommend stopping in at least once!
You could also look into a T-Bones game. It's in Kansas City, Kansas and is a fairly easy drive from everywhere in the city. It's a minor league team and the games are fun and cheap! There are lots of shops and restaurants around in the outlet mall.
As far as Wonderscope and Kidscape, they are fun (well Wonderscope is only okay actually) but if you only have 2 days, I would skip them.
The Plaza is also a good location to stay b/c it's close to a lot of things, including downtown. It's mostly shops and restaurants, but it's nice to walk around and look at all the fountains, etc. One of our favorite restaurants in Blanc, gourmet burgers that are way yummy! They have a nice kids menu and everything is seriously awesome! Andre's is also right off the Plaza and has the best quiche I've ever tasted! They have a lunch menu each day but it only borders on being kid friendly. BUT, their pastry case is to die for and you can always stop in for just that!
There are some parks close by too. Loose park is close and has a giant rose garden and playground. Brookside is just South of the Plaza and is another adorable area to visit. They have a fabulous children's bookstore called The Reading Reptile which is worth a visit if you are looking for things to do. It's locally owned and operated and has things to play with (including a ride on pony that cost a dime!!) and TONS of books to read. Next door is fabulous 5 and dime store too. The Roastarie is a local coffee shop also located in Brookside.
I do not recommend the zoo. It's not that great. The Polar Bear is awesome and my kids love the zoo but honestly, yours is way better!
I tried to include all of our local favorites b/c that's my favorite part of traveling. I always want to visit the local places because we have all the same chains as other people! ;)
Have fun!!