You'll both love the Corning Museum of Glass. http://www.cmog.org/
The glacial geology of Watkins Glen is very interesting.
Geneva and Canandaigua each have nice B & B's.
US 20 is a good alternative to the Interstates.
There is a lock on the NYS Barge Canal (formerly Erie Canal) you can visit in Macedon. My DW grew up in Fairport which has a lift bridge over the canal.

You have chosen an amazing place to vacation to during the best time of year. We are always happy to help visitors with their vacation plans and have come up with a few great ideas for you:
1st night/ 1st day:
Treat yourself to a lovely stay at the Glen Iris Inn overlooking the picturesque Middle Falls of breathtaking Letchworth State Park. Spending a few hours the previous evening and in the morning will allow you time to see the sites and enjoy a hiking trail or two. Stop for lunch in either of the local historic towns of Mount Morris ( QuestaLasagna is wonderful with a quaint atmosphere and homemade pasta) or Geneseo ( Bank Street Cafe offers a variety of juicy burgers) before taking the east 1 hour drive the Corning Museum of glass around early afternoon.
After enjoy the history and artistry at the museum we would recommend taking a trip to Ithaca for the night. You had mentioned Watkins Glen one of the amazing State parks the Finger Lakes has to offer but Ithaca has 3 of these parks that can easily be explored in a day.
2nd night/ 2nd day:
Spend the night in Ithaca where their slogan is "Ithaca is gorges" and they have a lot of gorges to show off. After breakfast stop by the local Wegmans to pick up some great local goodies for a picnic lunch and you are off to explore. The first state park you will find heading out of Ithaca is Buttermilk Falls, the second will be Robert H Treman. Both of these parks offer an array of waterfalls as well as great swimming and river walking opportunities. On the way up the West side of Cayuga Lake along Route 89 you will find the 3rd park of the day, Taughannock Falls State Park. The 215 foot (66 meter) waterfall you will find is one of the largest East of the Rocky Mountains. The rest of the drive to Geneva shows the full beauty of the Finger Lakes with a magnificent Lake views and rolling hills of fields. Geneva is a great little town to investigate with great options for a relaxing dinner after all of the hiking fresh air of the day.
3rd night/3rd day:
After a restful night sleep it’s time for a relaxing day to take your time and Tour the Towns of Geneva and Canandaigua along Routes 5 & 20. The trip through small villages and by old farm houses is a vacation in itself. Canandaigua offers a Main Street full of local shots, galleries and restaurants. Lunch at Simply Crepes is always a treat followed by Gelato on the Lake at the Muar House Cafe. The New York Wine and Culinary Center provides a look into the abundance of exceptional wine made in the Finger Lakes. Continuing along Routes 5 & 20 and south on highway 390 you will be right where you started in the town of Geneseo. At this point for your final evening we would love to be your friend in town while you rest up for the trip home the next day. Geneseo offers amazing local dinning to end your trip around the Finger Lakes.

If we can assist you with more information and details about this or any itinerary you decide on we would be honored to help you enjoy the Finger Lakes Region.

We were just in Ithaca. We did not have time to visit the waterfalls, but spent our short time there at Cornell University. It is a beautiful campus. I understand there is a museum on campus.

We stayed at the Country Inn and Suites. It is at the south end of town near Buttermilk Falls. Very, very quiet room, nice free breakfast bar and one of the better hotel pools (warm, too) I've seen in a while. Hot tub was immediately adjacent to the pool and also nice.