Our newest hotel is the Embassy Suites which is #1 in the Trip Advisor ratings, they have the pool & breakfast you're looking for. There is a shuttle that takes you to Main St. for shopping (antiques, gifts, lots of "girly" stuff). As a St. Charles resident I haven't stayed there but the facility is brand-new and well-regarded.
If you have preteeners you might want to check out Dave & Buster's just across the river in St. Louis County. They have a gameroom in back and pretty good food to boot.
There are also some hotels in Earth City (also across the river from St. charles) which were rated well in TripAdvisor, like the Residence Inn on Rider Trail South. If you have boys, this one's practically next store to where the Rams practice field is located.