And Friendship Shall Combine
I know for some of you this will sound like sacrilege, but I do think that a single premise combined from the "best" elements of the three series could have been enormously successful.
As far as the "home" setting of the Lewis Barnavelt series, neither other series matches (or even tries) to live up to the wonderful, evocative Victorian house. The Uncle Jonathan and Emerson characters are really reflections of each other, with some distinct variations, of course, but serving similar functions in the stories. Likewise, Miss Eells and Mrs. Zimmermann are also semi-identical "twins" from series to series. And, of course, Johnny Dixon, Anthony Monday, and Lewis Barnavelt, for all their superficial differences, play the same basic role in each series. The series are all set at a similar time, in similar nostalgic American towns, etc. They all use the same basic formula of pre-teen boy and older mentor figure solving supernatural mysteries together.
It's interesting to think how John Bellairs might have approached his writing had he only ever wanted to write one series. I honestly think he could have continued writing the Lewis Barnavelt series, and still explored much of the characterizations and stories seen in the other series. In order to explore all the stories he wanted to, as well as incorporate characteristics from other series into the Barnavelt books, would Uncle Jonathan be a less effective magician, a little crankier, and a university professor to boot? Would Mrs. Zimmerman become a librarian who dabbles in magic on the side? Would Lewis become a little more adventurous and less timid? Would Lewis have been named Johnny Dixon, since that's a more marketable, catchy name to sustain a long-running series?
By focusing on one series, the Bellairs books might have been more "neatly wrapped," and thus easier to market and sell, and to spin off into a tv series, film adaptations, etc., if they had followed the adventures of a lone protagonist.
Anyway, that's my two cents on the subject. As a writer myself, I don't find the three series so distinctly different that they couldn't have all taken place in the same creative universe. Don't get me wrong: I like all the books and am very grateful for them, but I love to play, "what if. . ."