Susie,
You're neice is super lucky! You'll have a great time.
Your plan is a solid, no-hassle Paris Metro/RER plan. If you went with Billets Ile-de-France for the Versailles & CDG inbound trips, you'd save only about 3€ vs. the 5 zone Carte Orange Navigo Découverte that you're already planning on. Thus, I'd totally go with your initial purchase plan, since I'd say the hassle of messing with tickets "costs" more than 3€.
Since I can't help offer any advice on trains, how about I make that up with some suggestions on great places/things to do in Paris:
- Lunch at Alcazar - really cool, modern expansive dining room tucked away north of St. Germain. Lunch menus at 19, 26 & 32€.
- Chausson aux pommes/tartelettes aux pommes at Poilane - famous bread maker is also the master of buttery, apple pastries. I love places that do nothing, but their specialty, which means they do that one thing very well. This place is one of them.
- JP Hévin Chocolatier - One of the master chocolate makers in Paris. A good variety of hand crafted chocolates to try and bars of chocolates from cocoa grown in specific places. Buy a few and do a chocolate tasting: you'll be amazed by the differences.
- Lunch at Benoit - classic French cuisine in a traditional bistro on busy pedestrian street just south of Centre Georges Pompidou. Michelin one-star. Dishes of note on the lunch menu: Petit Paté chaud de lapin sauce civet, Savarin au rhum creme fouettée (you'll be happy & warm after eating this cake ;^)
I've compiled the locations of the above on a Google Map:
Ben's Paris Tour.
Have a great trip!
Ben