My rule of thumb is to never spend less than 3 full days/4 nights in any place unless it is just an overnight stop between A and B. Note the 'less than', it is a minimum I think it takes to really be able to see/do anything worthwhile. Most people would agree for example that you need more than 3 full days in a place like Paris, Rome, London, etc. unless you have little interest in what such places have to offer the traveller.
I know people say that for them, 'one day(or two) in X was enough'. It may well be but that means they are moving more and spending less time in total IN places. If I think a place will only hold my interest for a day, I skip it entirely unless I can do it as a day trip from somewhere I do expect to want to spend more than 3 days in.
My preferred method is to just go to A and stay until I am ready to leave. Then decide where to go next. Rinse and repeat until either the time available or the funds available run out and then go home. That only works if you are willing to wing it as you go however and most people aren't willing to do that based on their belief that it will cost them more. It may or may not (you might be surprised) but they believe it always will.
In your case, I would fly to Crete and wing it from there with the knowledge that I had a return ticket from Paris on X date. That return flight would be the only restriction on where I would go and when.
I approach travel as an adventure. An adventure however requires two things by definition, risk and the unknown. A tour on the other hand, whether booked through a tour company or self-booked (as in a pre-planned and pre-booked itinerary) is not an adventure, it's a tour plain and simple.
Pre-booking and itineraries put blinders on us to opportunities that can arise when we travel. I have seen first hand many examples of people who when presented with an opportunity say something like, 'oh, I'd love to do that BUT I have a hotel reservation; flight booked; etc. and I CAN'T do that.
Travel to me is about freedom. The freedom from everyday life and all the responsibilities we all have. We are conditioned to live with schedules. I have to be at work at 9am. I have to keep an appointment, etc. Vacation time to me is being able to get up in the morning and say, 'so what do I want to do today and where?' Move on, stay where I am, go somewhere someone suggested and I had never even heard of, all are possible UNLESS I lock myself in to a 'plan'.
I never understand why people want to throw that freedom away before they even leave home and plan everything ahead of time. There is no law that says you have to decide ahead of time whether to go to any given part of France etc.
Suppose you meet an Italian couple staying at the same hotel in Crete with whom you become friendly. Hearing you are on your honeymoon, they say, 'Ah for a honeymoon, nowhere is better than our home on the Amalfi Coast. Why don't you come stay with us this weekend?' Are you gonna say, 'Oh we'd love to BUT'.
You may find that example far fetched and perhaps it is, but such things do happen. You can be open to such opportunities or you can be on a tour. Your choice. I have heard a person first hand turn down an opportunity for free transportation and accommodation for the Running of the Bulls in Pamplona with just those words. I've also heard someone else say, 'I'm free to go, when do we leave.'
Or you may just find yourselves saying, 'oh we love it here on Crete, I WISH we could stay longer.' Well why can't you? All you would have to do is extend your hotel stay or find another hotel on another part of the island.
Dare to be adventurous. It's easier to expand your comfort zone than you may think it is.