I'd like to see Hamburg, where I was born. And the other main focus of this trip is taking a boat ride down the Rhine and experiencing Die Lorelei... and other places that are not necessarily some fake tourist-oriented attractions.
If you want to avoid gobs of tourists in places that aren't everything they're thought to be, the two main offenders are probably Rothenburg ob der Tauber and Neuschwanstein. But since these places are both in Bavaria and at the very end of trunk railway lines, it's very unlikely that they will be stumbled upon, especially if your focus is Northern Germany and the Rhineland (kudos for a refreshingly original itinerary!!)
Hamburg is an interesting place, and different from most other German cities. Nearby, you might want to check out Bremen and smallish old-world Lüneburg
The tourist nest on the Rhine is Rüdesheim - but you might want to check it out anyway to see if the attractions there appeal to you. The cruise is great - but you don't need to do more than the 1.5 - 2.5 hours it takes to travel from Bingen (southern end of the scenic part) to St. Goar or Boppard in the north. Be sure to travel from south to north (downstream) unless you want to waste a lot of boat time chugging against the current (it's about 40% slower from north to south.)
The trains around the Rhine are excellent. Ferry crossings help you get across (no train trestles between Koblenz and Mainz!) See map:
http://www.loreley-info.com/eng/rhein-rhine/walking-hiking.php
The trains around the rest of Germany are excellent too.
You could easily spend about a week in the Upper Middle Rhine area if you were to include visits to the Mosel Valley as well as a couple of additional peripheral cities (Cologne? Trier? Mainz? Frankfurt? Boppard is an excellent, not-too-touristy Rhine town with a central location for doing most of the outings you might do - it has lots of accommodations (some right on the river) and restaurant choices, some Roman ruins, an exciting trail network including the "Klettersteig", an awesome chairlift, and a nice old-world vibe - and it's a great base for seeing the lower part of the Mosel River as well (Cochem, Burg Eltz.)
And a week in the north around Hamburg is doable as well. Lübeck is another popular outing. So are the northern beach areas.
With a two-area focus you likely do NOT need a railpass. There are local day passes available in both areas - and in Boppard, you will get a FREE pass for the trains that is valid throughout your stay there.
The Rhine towns are very close to FRA. You might find it smart to fly into FRA and out of Hamburg, or vice-versa.
Saver fare tickets between your Northern and your Rhine areas can be bought in advance at the DB site; Day passes for local travel and short trips to the airports are best purchased at the local train stations.
Welcome to the forum, Vicki. And... Happy planning.