If we waited until after 10:00 AM to travel, crowds on trains were often significantly reduced.
Augsburg
Schwäbisch Hall
Rothenburg ob der Tauber
Regensburg
Burghausen
Freising
That still applies. For example, I can tell you from frequent experience that the trains from Augsburg to the north (RE 16 towards Nuremberg) are half full, starting with the 9:32 train. It gets fuller after the transfer to the RE 80 in Treuchtlingen (-Ansbach-Steinach-Rothenburg), because GoAhead has not managed to provide full-length trains even more than a year after they started operating. But here, too, I would only expect very full trains during the Bavarian school vacations (Easter: 22.3.-6.4, Whitsun 18.5.-1.6, summer 26.7.-9.9). I wouldn't expect a big rush for the other connections after 9am either, except Nuremberg-Regensburg. However, if you are coming from Rothenburg, you often have 20 minutes to change trains in Nuremberg. I would go to the platform immediately. Assuming you take the train dep. Rothenburg at 10:05 and arrive in Nuremberg at 11:21, the RE 40 train to Regensburg, dep. 11:43, is sitting already on platform 20 (since 11:15), but is certainly not yet full. Have a good journey!