+1 on Booneville to St Charles being the most scenic.

My wife and I rode it last May and thought it was a great experience. I think it depends on how you like to tour. We cycled out of our driveway to the nearest Amtrak station, took trains to Sedalia, cycled to Clinton, then back to St Louis. A couple days we rode 50 mi, but other days we'd make side trips, or just hang out and experience some town all day. There are some very challenging ( for us at least) climbs out of the river valley. The Katy Trail is 230 mi. Our total trip was about 400 mi.

I'd second the idea of checking ahead for services, especially if you're considering inn-to-inn in the off season.