2 Weeks in Switzerland, Italy, France in June

I would eliminate Cinque Terre and do some hiking in Switzerland. It is eating up a lot of time in your itinerary. In fact, I'd make it an all-Switzerland trip, but you must have chose both for a reason.

So 13 nights and in each plan and I counted only 7 full days. That is way out of balance; you need to stay longer in fewer places, 4 places max. You also need to factor in train times. Not to buy tickets, but quick schedules here:

https://www.bahn.com/en

That will tell you that Annecy to anywhere else on the list takes too long.

hey hey SMS
are you getting a better airfare R/T with geneva? are tickets purchased?
we took a train from paris to geneva and spent 2 nights. took a cruise on the lake, found a taxi to give us an hour tour around part of town along the lake and back to flower clock, had lunch at an outside restaurant in gardens overlooking lake. i was not that impressed with geneva, business center during daytime then closes up.
we hired a private taxi to annecy, about 40 minutes, for 95E. great transport, door to door service, since train would have taken about 2 1/2 hours. we loved annecy, stayed 6 days. it's beautiful with the mountain views, the lake, the city center. we hired the same taxi for a 5 hour private tour around to small villages around lake, attractions in annecy. the farmers market, the food. train back to paris.
your itinerary is over zealous to me, i would stay closer to annecy with the smaller towns closer on train, the going to lake come 9-10 hour train ride, plus cut out cinque terre and consider another trip with northern italy as a later trip.
check out the town:
aix-les-bains, about 40 minute train ride, a spa town
chambery: city of art and history, elephant fountain, pedestrian streets, cathedral. bus is 40 minutes
bourget lake, glacial natural lake, mansions & castles 50 minutes by bus
lyon: train about 2 hours, roam thru the center, have lunch, enjoy the sites
stop at a TI kiosk in city center and see what is offered and if you like anything. spend more time sightseeing instead of in a train/station.
my own opinion, your train travel is long hours i think you're trying not to do plus stay away from crowded cities. so much to offer around the area. good luck
aloha

Hi! Thanks for your reply princess! Super helpful. Could you share the taxi service you used to get to Annecy? Unfortunately, yes we booked flights already and they were nearly half the price of nearby cities in Italy. Thanks so much for your recommendations, I will look into those cities.