We spent our honeymoon doing a train and cruise journey for about 4 weeks - train overnight down to Madrid, couple of days in Cadiz, caught the boat there, did north africa and ended up in Athens, then spent a few days in athens, ferry to Italy, train to Bologna for a few nights, then back to Paris and home.
Was amazing - and can recommend all the places as nice places to visit (albeit sad that North africa is off limits these days). We got a deal for the overnight bit from paris to madrid so were able to upgrade to first class for £20 each, meant we got a cabin for the two of us only with a teeny bathroom en suite (you could sit on the loo, brush your teeth and have a shower at the same time if you were so inclined - it was teeny!) plus a delicious 3 course meal and house wine in the restaurant car was included, so we had something to do in the evening and would have had to have paid to eat anyway, so was a great deal - so worth looking out for if you are doing any of that sort of thing...
But have a look at cruising too - it can be a fab way to travel and see lots of places but without the inconvenience of having to unpack lots! They also have plenty of tours and things you can join in with if you fancy or you can do your own thing. Joining a cruise on the north coast of the med by train would mean you weren't wasting time travelling in the rougher seas to get down there. We went with Swan Hellenic who specialised in older travellers but we had a fantastic time and were treated incredibly well. Plus they included lots of stuff, and we got it for half price, there are often deals, so don't be put off by the initial price! Combining cruising with the train worked really well for us so I can definitely recommend it.
The other thing to do is to look at are companies like Voyage Jules Vernes and others that organise tours by train or to areas you are interested in, see what sort of itinerary they offer, as then you can use them as an idea of places to go and how long to stay in places.