"Would we be better off to just take a train to Rothenburg and spend the day and catch a train back to Munich in the evening?"
The ride itself would take up most of the day.
"I've read a couple commentaries that state the Romantic Road really isn't that big a deal unless you actually get off and explore the small towns which we clearly won't be able to do on a bus and train."
It is true that you cannot get off the RR bus for a reasonable amount of time to explore. If you do, you'll be in that town for 24 hours waiting for the next RR bus.
But the train is another matter entirely. It is perfectly possible to visit most of these towns by train and to see 2-3 towns in a day (which is all you have time for in a day anyway, really; doing the RR by bus or by car in one day is a ridiculous undertaking.)
If the northern RR towns (Rothenburg, Würzburg, Weikersheim, etc.) interest you, I'd recommend staying in Würzburg (a major train hub.) You can be in Weikersheim and in Rothenburg in about 1 hour. And as Martin so accuratly points out, "such towns exist almost everywhere, you don't have to follow the RR to see them." The old-world towns of Ochsenfurt and Iphofen are even closer to Würzburg - and you don't have to share them with the international tourist horde that only knows about Rothenburg. Why not see them as well? If you think the RR has all the great towns, just check out these photos to understand how mistaken this notion is:
IPHOFEN
OCHSENFURT
BAD WINDSHEIM'S VERY AMAZING FREILANDMUSEUM (a collection of historical rural Bavarian buildings that were rescued and reconstructed and now provide a window on life there over the last 6 centuries - also about 1 hour from Würzburg.)
And then there's Bamberg - the old town there is a UNESCO World Heritage site - less than 1 hour from Würzburg:
BAMBERG
To the south, the RR towns of Nördlingen, Harburg, Donauwörth, Augsburg, and Landsberg am Lech are also well connected by train. It would be easy to spend 2-3 days in this area as well.
This rail line diagram shows how extensively Bavaria is served by train. You can use it to locate the towns above and plot out where to stay and how to reach the towns that interest you. Red lines = hourly (or better) train service. Blue lines = river valleys.
BAVARIAN TRAIN ROUTES