It's a honeymoon - presumably, you want to spend more time on top of your wife than at train stations/airports.
For only 2 weeks, I would limit it to 3 independent locations max or stick with a limited area that you can easily tour by car or train. To properly appreciate the "great" European cities you need more than 2 days.
You can, for example (not suggesting this itinerary - just a "what if"), do 4 days in Barcelona, 5 in Paris and 5 in Rome or 2 of those and a Med cruise. Alternatively, go to Italy and do a tour heading north from Rome. Don't pack in too much, enjoy each locale, plus it's your honeymoon - you can save the 12 cities in 12 days tour until you are 65...