Which one is the best is totally up to you, based on your interests, willingness to long time travels, etc.
Like you said

:
Personally, I find planning one of the most enjoyable aspects of zoo touring. The puzzling with distances and time delays, opening hours, attractions, comfort and price of lodging, etc., what fun it is.
Just a few extra thoughts on your plans:
If you want to take the train from Karlsruhe to visit Walsorde, you could possible beter take Walsrode instead of Hannover as your overnight destination (it's roughly +1 hr). There is a hotel right across from the park entrance and bus 511 will take you there from the train station. Left your luggage at the hotel, enter the park from the opening hour and pick it up when leaving (I do not know if the zoo has lockers in case you have your luggage with you).
Your day Wuppertal - Krefeld - Duisburg: I guess all three zoos are a first for you, so that is a harsh day. Your time table will be something like this:
Wuppertal Zoo opens at 9:00 am
Walking Wuppertal Zoo – Wuppertal Zoologischer Garden Bahnhof 10 min
Train Wuppertal – Krefeld 1:15
Tram Krefeld Hauptbahnhof – Zoo Krefeld 30 min
Zoo Krefeld 9:00-5:00 (animal buildings close at 5:30 pm!)
Tram Zoo Krefeld - Krefeld Hauptbahnhof 30 min
Train Krefeld Hauptbahnhof – Duisburg Hauptbahnhof 30 min
Tram Duisburg Hauptbahnhof – Duisburg Zoo 30 min
Duisburg Zoo closes at 7:00 pm (animal buildings cloase at 6:30)
So that gives you roughly a time frame of
Wuppertal Zoo 9:00-11:30
Transport 11:30-13:30
Krefeld Zoo 13:30-15:30
Transport 15:30-17:00
Duisburg Zoo 17:00-19:00
I counted the time very generously as far as tram connections are concerned, but you always loose some time searching or miss one that leaves right in front of you.
Wuppertal is a fairly large zoo, and one of the main attractions, the lion savannah and house, are farthest from the entrance. It is also the zoo with the most buildings, and because it is the first of the day you risk being immediately pressed for time.
Krefeld and Duisburg are smaller, but the latter consists of 2 parts that can only be crossed at 1 point.
I think 2.5 hours Wuppertal and 2 hours Duisburg is on the very low side anyway. I have visited them both regularly and 3 hours for each seems to me to be the minimum.
Kronberg isn't a very large zoo and there are hardly any accessible buildings, so 2 hours will do.I don't recall seeing lockers, so keep in mind it's a very tough hike with some really steep climbs through the zoo with your luggage.