Congratulations!
First, what month are you going?
Second, two weeks and 3, possibly 4, countries is, IMO, too many countries. Remember that each day moving from country to country takes a (full) day away from visiting a country. So with 3 countries you lose 2 days and with 4 countries you lose 3 days. Changing locations involves more than the train or flight times....checking out of lodgings, getting to airport or train station, possible security check time (airport, 2 hours for sure), travel time, getting to new lodgings and checking in. And I suggest you count nights in a place, not days. It works out better in planning your trip. (Sounds odd, but it really does work.)
"Off the beaten path" exploring is a bit hard to do as so many people are traveling, and "influencers" have in some cases highlighted places that used to be more "hidden", but aren't anymore. That being said, I have found that having a car and driving through the countryside of a country often leads to finding a small town or village that is charming and low key. Time of year also makes some places more "off the beaten path" during certain times of the year.
What are your interests? When you picture yourself in Europe, what do you see? Do you have any long-time wishes regarding any place in Europe, such as the Eiffel Tower, the Coloseum, Big Ben? This sounds like a corny exercise, but it does help!
Even in popular places with lots of other tourists, you can really enjoy yourselves. Paris is, rightfully so, considered the most romantic of cities. My husband and I have been there in our early 30s, our 40s, 50s, 70s and even at 79 and 80. We have been there in April, May, June, July, August and September. It has ALWAYS been wonderful! I would definitely spend 5-7 days there, as there is so much to do and see, and even doing nothing there but strolling or sitting at a cafe feels special (5 days in the city with 2 other days for day trips).
The big three cities, London, Paris, Rome are all worthy of a week minimum. However, if you pick just 2 locations, whether it is 2 biggies, or a biggie and some countryside, or even all countryside, your honeymoon will be great. For me, I would pick one country and spend half the time in one or two major locations and half the time in one or two smaller towns/villages/areas, or places with a different weather patterns (e.g. Paris and somewhere in Provence, or Paris and the Riviera).
My best advice is to close your eyes and pictures yourselves in Europe. What are you doing? What do you see when you look around yourselves? Put some of these pictures together in your mind and you may discover your location.
Best wishes and enjoy your honeymoon!