I attend a fair number of tours and regional productions. The talent pool is often the same for each, especially for the bigger regional houses. When I lived in the Chicago area, regional houses often had productions that were as good, and sometimes better, than what you would see on tour. Living in central Indiana, both regional theatre and touring productions can be hit and miss.
Indianapolis, Bloomington, and West Lafayette are not first tier markets for tours. They are often non-equity, and some (Legally Blonde, I'm looking at you) have atrocious production values, especially for the prices paid. Indianapolis Repertory Theatre, on the other hand, always has quality productions. The problem there is that the seasons are often dull and feature shows that can be real snooze-fests. last season's Sense and Sensibility stands out as being especially sleepy. Although, I have seen some truly great stuff there as well. Beef and Boards offers more butts-in-seats shows, but the production quality can vary a bit.
In all honesty, I have been preferring to see the productions put on by the various university theatre departments as of late. They have more bang for the buck, attending supports the education of future theatre workers, and some are just damn good. IU, Purdue, and Ball State have some truly gifted young professionals entering the industry.
To answer your question, I think that there isn't a preference for me of one over the other. It will depend entirely on the production that is being produced. I can tell you that I am all but certain that the upcoming regional production of Legally Blonde will almost certainly be better than the tour that has been crossing the country as of late.
