Well, I watched the 3-hour cut. Absolutely stunning cinematography and production design, and wonderful performances from pretty much everyone, memorably bringing to life an eclectic group of characters. However, as the film moved closer to the end, I began to suspect I had to watch the 5-hour version right from the start. If I had to guess, I'd say Bergman cut fairly little from the first half of the story (pre-Bishop) and quite a bit from the second half, as the story seemed to me quite rushed there: for example, Emilie tells her children she married the Bishop out of love (even if it wasn't entirely true, it seemed to me that she had some clear feelings for him), but not even 20 minutes pass before she tells her mother that she loathes him. And I also thought he'd be more malicious than he actually was; he does have that one big scene with Alexander where he punishes him, but overall I seriously expected worse from him considering how strongly Emilie comes to despise him and how uncompromisingly he is called a villain in every description of the film I've read. Additionally, I have no idea why the hell Fanny is in the title when she's on screen for about 20 minutes total and doesn't do or say anything important during that time.
In short, I thought it was a very good, amazingly beautiful film, but I'll wait to form a final opinion on it until I see the 5-hour version.