I have a few ideas on this…
We spent (all of) last September visiting Portugal, Spain and France. Our first Tourradar tour (Portugal) was 9 or 10 days. We loved it, felt it was great, and we got to see a lot of places (Lisbon, Cascais, Obidos, Sintra, Fatima, Porto) and it didn’t feel rushed at all, actually more of a semi-private driver-led tour with only 3 people (my wife and I, and a really nice lady that we became friends with and still correspond with to this day).
Our second Tourradar tour (right after the Portugal one) was of southern Spain, for another 9 or 10 days. It was with a bigger group (about 14 people) was very rushed but we visited Madrid, Valencia, Granada, Cordoba, Seville and Barcelona but only spent 2 days in each city (so basically living out of our suitcases), walked a lot while being led by the tour guide that stayed with us for the duration of the tour.
Then we visited France on our own for about 9 more days. We went to Lyon, then Avignon (for 2 days each). This was also a bit rushed but we assumed (incorrectly) that the pace of the tour in Spain would also be ok in France, but we had all most of our time to ourselves to tour. Then we spent 5 whole days in Paris, where things slowed down (meaning a much more leisurely pace) and we could really enjoy the city. I still remember the little boulangerie around the corner from our hotel in the 6th arrondissement (Saint Germain Des Pres) where we’d get breakfast every morning.
The total travel time between countries is close to the same whether by plane or train, but on the train you can relax and not deal with all the security, luggage, moving between terminals, etc… that are part of air travel. And you can actually relax while making last minute plan for the tours in the next city - and the train goes close to downtown so you’re closer to center-of-town hotels if that’s your thing. Something for you to consider.
Now, knowing this, we decided to make our next trip, again all of next September, all in Italy to get around by train as much as possible. We’ll be staying in Venice, Florence, Naples, Sorrento and Rome where we’re staying at a rented apartment with friends coming off a cruise. We’re booking less hotels but more day trips to get longer stays in any one place and get to feel where we are (not just blow through it); day trips from Florence to Bologna/Modena/Parma, and a part of Tuscany on a day-long tour, from Sorrento to the Amalfi coast, from Naples to Pompeii.
So that’s our past experience and adjustment for our next trip. We’re newly retired and still pretty active, but don’t want to spend “vacation time” dealing with logistics of travelling between cities, hence one country and taking trains everywhere (as much as possible).
Hope I didn’t go on forever, and that you can use some of this information to make the decision on how you want your trip to be. Your gut isn’t wrong, but you (should be) able to return to Europe to see other countries in the future. I suppose your other option is to get a Eurail pass and hoof it around Europe without any agenda, stay at youth hostels, and take it all in, like we used to do right after college…