I have had good experiences with the Delta Atlanta hub (but I haven't tried flying with a dog through there).
Yung-T, Stuttgart. No Quarantine,,,otherwise, I wouldn't go. Most the continental EU doesn't require quarantine. Most island countries do (Ireland, England). I am starting to freak about it. I can't get a direct flight to Stuttgart, and can't bare to make her do a layover after 9hrs. So hoping to get someone to pick us up in Frankfurt. Although I can get her on the trains sitting next to me, but then I couldn't do that with a whole bunch of luggage and her.
Have you thought about maybe renting a car? Frankfurt Airport to Stuttgart is about a two hour drive. You should be able to get a car big enough for you luggage and dog for about 150€ a day. Just a thought.
Is there a drop off fee for one-way, like in the States. That can be steep. I can easily drop it off at rental at the Flughafen Stuttgart. I can probably ship my footlockers, maybe get down to one carry on. But if the drop off fee isn't huge, rental sounds like the best way. Except I might be too tired to drive safely on the autobahn for my first time; maybe not a good idea.
I've never actually rented a car, but I don't think there is an extra drop of fee for one-way. I believe 'Sixt' is the biggest car rental company in Germany. You should be able to find all the infos you need at http://www.sixt.com Whether or not you'll be too tired to drive you'll have to decide yourself .