I dont think you can say which is better than the other, they are different. I have fished The Missouri numerous times and I enjoy it because it can be more stalking individual trout & challenging. The Caddis can be so thick with fish rising everywhere you dont know where to cast next and what fly to use because you have used every caddis in your box.
I have also fished the Big Hole and caught Rainbows, Browns & Grayling the same day.
Also the Beaverhead is just awesome,Huge rainbows on tiny nymphs.
The Ruby is a small intimate little stream with gorgeous browns, but with challenges of it own with access restrictions.
The Madison is like they say one big riffle and fish can anywhere, the edges, or the middle & then fished the Yellowstone then the Jefferson.
We fished all these rivers in a week and caught fish in all of them. We were guided on some them & some not. It wasnt the numbers of fish or the size of the fish(because 1 river we only caught the one & I probably think of that 1 more than any of them) that made the trip, it was the scenery, the different water, the towns, the flyshops & the people.