We tried not to stay in eu cities for too long when kids were at that age - perhaps a couple nights and then 4-5 in some outdoorsy area with pool places to roam and stretch (former IC now kempinski berchtesgarten was awesome with young kids)
Looking at hyatt map maybe vienna is an option - its a green and rather child friendly city and you can perhaps rent a car or take a train for few days in the mountains...
I like munich with side trip to southern Bavaria
Lisbon is another possibility or GH istanbul mentioned above although exploring istanbul with a toddler may be challenging.