Short day/two trips from Paris

In my opinion, the cities you mentioned are too far away to be an enjoyable day trip.
Good day trips from Paris include:
Chartres
Giverny
Reims
Chateaus in the Paris area, such as Vaux-le-Vicomte, Chantilly, or Fontainebleau.

With 9 days in Paris (and that may not be 9 full days), a 3-day trip probably doesn't give you enough time in Paris (especially if this is only your first or second time in Paris).

A 2-day trip gives you more choices than those I've listed above.

We did a 3 day trip by train to the north of France. Stayed in Bayeux for 3 nights and then we did a full day tour to the Beaches of Normandy and the American Cemetery..... then another 1 day tour to Mount St. Michel.
It was a wonderful 3 days and we saw beautiful scenery while on the trains and enjoyed the small town of Bayeux also.

I agree with Kent, those destinations are a bit too far. London is a quick and easy 2 to 2.5 hour train ride and a fun way to spend breakfast in Paris, and be in London for lunch.

Fast trains from Paris to either Barcelona or central Switzerland each take 6 hours one way and cost a pretty penny, unless booked about 1 - 3 months in advance. If you took a train that far, I would fly home from that city, not return to Paris. Train travel time is shorter to Brussels, Bruges, and other hotspots of Belgium, under 3 hours each way, and also not cheap unless booked ahead. If you want an overnight destination within France, then consider Rouen (1 hour) and Honfleur by train and bus from there (via Le Havre).

Have you been to Hon Fleur? If you are looking for a quaint village with rich history, Hon Fleur has that. Very old, beautiful, and friendly. A few touristy shops, but not many. Deauville is a 30 minute busride away. Saw tourists from France there, but not from all over the world. Nice beach, but not very much to do in town.

We are in a similar situation but different city this summer. We have 19 days in London and have visited London many times before. We challenged ourselves to come up with new things to see in and around London (having a lot of success with that) AND book a mini vacation away from London. To choose where to go for mini vacation within a vacation we looked at skyscanner for destinations that were less than $100 pp/rt, non-stop, and to city we wanted to see. We had several to choose from and after a lot of hard choices, picked one for a 5 night stay. Best wishes for finding something interesting and doable. BTW, I like the northern France ideas others have given you if you don't go too far from Paris.

Take a look at Paris to the Past by Ina Caro, describing many historic places you can easily reach by train from Paris. Some of them will be "touristy" but others not so much. As I recall, they all looked like day trips except La Rochelle on the Atlantic coast.

Finding a place that meets all your criteria -- contrast with Paris, village-type setting, yet reachable by train, preferably with Alps in sight, not "touristy" -- will be a challenge. And it will make a difference, in terms of how much travel time you can take, whether your trip is 2-3 days or 3-4 days.

How about Amsterdam? Easy, fast train connections and a very different experience than Paris. I think Amsterdam is fantastic. Not a village for sure, but very walkable and rich in history as you have noted.

If you want to stay in France and fly Paris round-trip, the possibilities are numerous using the TGV. Each region is different and there are charming towns in all of them. As Laura pointed out, going to Switzerland or Spain would really only be worthwhile if you can fly open-jaw.

For quaint and other country I'd choose Delft with day trips to Amsterdam and The Hague or Ghent with day trips to Bruges and possibly Antwerp or Brussels.

In France, if you like champagne, Reims/Epernay. For very different, Colmar/Strasbourg.

There are dozens of great day trips to small cities and villages within an hour of Paris by train. Here are some we have done recently: https://janettravels.wordpress.com/category/day-trips-from-paris/

Some others include Rouen, Reims, Auvers sur Oise, Chartres.

Amsterdam is 3.5 hours away by Thalys and a 3 night side trip there would be lovely although it would be best to fly into Paris and our of Amsterdam to save the backtracking. Amsterdam has an entirely different atmosphere from Paris with its canal houses and canals and bridges. Lovely place for a 3 night/2 day trip. Alsace training to Strasbourg would also be a nice 2 night side trip. When we had a spare 5 nights in Paris a couple of years ago we went to Normandy which was terrific.