Haven't seen the Mill Creek set, Chas, but Ivan Shreve's "Thrilling Days of Yesteryear" blog site reported that opening/closing theme music has been replaced on all of the "Bonanza" episodes. The good news is that Mill Creek collects all of the 31 public domain "Bonanza" episodes in a single collection and throws in the three PD episodes of "Wagon Train" as a "bonus."
The Brentwood/BCI Eclipse 20-episode set does include the original theme music and has decent transfers as well . . . . . it's, arguably, the best of the "Bonanza" PD releases, but it does not include all of the available PD episodes.
Given its name recognition, I'm suprised that an official Bonanza DVD realease from CBS/Paramount isn't on the radar, not even as a best of. Any reason to this?