I admit it, I am a TRAVEL WHORE! I always try to find the best way of raping the Airlines and Hotels, etc. to get the most out of my hard earned miles and points. With that said, my choices would be....

Moscow/St. Petersburb (AMAZING CITIES) The Hotels are outrageously expensive, but I was able to use my Marriott points at each of them. I flew into Moscow and out of St. Petersburg, also using my points. This was end of August/Labor Day a few years ago. However, in my experience and having talked to others who have been to both cities...You love one and hate/don't like the other, and it was true for me. I LOVED MOSCOW!

Whirlwind Scandanavia Trip (Stockholm, Oslo, Helsinki and Copenhagen) or any combination of each. Did this about 5 years ago and spent 5 days in each of the cities, using my Hilton points (Scandic Hotels). Loved Stockholm and Copenhagen, thought Oslo was BORING, but surrounding area was beautiful, and Tolerated Helsinki to the point that I left for two days and took the boat to Tallinn.

PARIS PARIS PARIS - What else can you say, most beautiful city on earth!

London - Love London! Go at least twice a year and do nothing, but the same old thing. Theatre, musuems, nightlife, rinse and repeat!

Finally, Marriott acquired these new trendy boutique-type hotels called AC. They are ALL over Spain and Italy and I think even Portugal. They are normally low tier level, meaning you could spend a number of nights in various cities for very few points. I would go back and do Andulucia over and over. Malaga, Granada, Cordoba, Seville, Cadiz, etc. Hell you could even do Madrid area and/or Barcelona!

Hope this helps and haven't read all of the previous posts, I know you have already ruled out some cities, areas, etc. (London). But good luck and enjoy!

Look at the interactive map of Delta and Skyteam and perhaps you will see where you want to go nonstop out of Atlanta?

Paris , and or Paris/London.
I have taken my kids to Europe, and both those cities fit your bill. The museums in London are great, your son will likely really enjoy the Natural History Museum, and right across the street is the Victoria and Albert Museum, both are excellant. The Tower of London with its included Beefeaters tour is fun and informative. And for an outside trip Warwick Castle is lots of fun, they have great jousting and catapault demostrations .

For Paris, well the Invalids War Museum ( there are ROOMS of armour , medival battle axes, spears, etc etc, , literally could spend hours just covering the medival stuff) this was both my sons favorite musuem in Paris.
Great daytrip, Provins, look it up, its a world heritage site, done up like a living museum inside the old walls, also , great shows, I saw the Birds of Prey show and really enjoyed it, its done outside, with real horses, camels etc..

Thanks to everyone for your help! After much debate, I think we're leaning toward Paris combined with a few days in Normandy. We may wait another year or two so that our son will be a little older and better able to appreciate the D-Day beaches and WWII history - for this coming summer, we will likely choose a destination other than Europe. But I've bookmarked this thread so that I can put all your advice to use when the time comes.

Think a bit longer:
AMSTERDAM
AMSTERDAM
AMSTERDAM

Wonderful for kids
Wonderful for walking
Wonderful for biking
Wonderful/easy local transportation
Wonderful big museums
Wonderful small museum
Super airport, easy from Atlanta
Good, interesting food
Great people
Easy for the lingual restricted
Wonderful any time of year
Easy to immerse yourself culturally quickly