Visited both last summer. Munich was absolutely awesome. Not a whole lot to do in Innsbruck. Did the Swaravski tour near Innsbruck. Nothing special. From Innsbruck we drove to Munich. We took the route given us by the car navigation system. It was the shortest distance but went through the mountains and was a longer drive time than taking the Autobahn. But the drive was absolutely beautiful. If you take that route, leave time to stop along the way.
In Munich, an evening at the HofBrau House is a must if you are breathing. Corny but alot of fun. (don't go if you do not like beer) Augustiner was also very nice. A roasted pork knuckle at the HauxenBrau near HBH was great. It rained the whole 3 days we were in Munich but we still loved it. Viktualian Marketplace is also much fun. The English Garden is also supposed to be great but with the rain we did not go. We visited there in August. English Garden next time.
Rottenburg on the Romantic Road was wonderful. Try to stay within the walled town if you can.
Frankfurt is not much more than a place to fly-in and switch planes, or attend a boring seminar. See as much of Munchen & the Romantic Road as you can..
Visit Munich and the Romantic Road. As the other poster so aptly describes Frankfurt: skip it. It was heavily bombed during the war and they decided not to restore as much of "old" Frankfurt as they did some other cities (like Munich). Black Forest is overrated, too.
Last summer we were in Innsbruck for my husband's work and then in Munich to visit friends. I've visited Innsbruck and Munich several times and like both, but honestly, Munich is much more impressive. Way too many things to do, like drink a beer near the Chinescher Türm in the English Garden or gaze at the Old Masters in the Alte Pinothek.
Used to live in Germany. I've never tired of Munich.
Just one biy of advice: Turn in your rental car before you stay in Munich. You will not need a car.