I'm glad you opened this thread. I haven't listened to "Blonde on Blonde" in a long time, and I have it playing now as a result of your reminding me.
Bob Dylan and his work are interesting subjects. I think it is difficult to say with certainty that any one record is his best, because his style changed so many times, much like that of the Beatles. Despite his emulation of Woody Guthrie in his earliest records, he never sounded like anyone else, and he was always ahead of everyone else, or perhaps rather, he was never in the same race with everyone else.
I like "Blonde on Blonde", especially songs such as "Stuck Inside of Mobile With The Memphis Blues Again", "Just Like A Woman", and "I Want You". It has what I call his "middle period" sound, with mostly electrically amplified instruments and a sound concentrated in the midrange. In my opinion that sound works better on some songs than on others. As to his lyrics, they can give the impression of opacity and imcomprehensibility, but for me they evoke striking images and impressions that linger long after hearing them. Dylan excites both the emotions and the intellect.
Great artists like Dylan sometimes leap ahead of their audiences, and by the time we catch up to where they were, they are no longer there. This happened to me when I was a kid and first heard The Beatles' "Revolver". I could not comprehend it at first, but the more I played it, the more I liked it, and it became one of my favorite records. If you are already a Dylan fan, perhaps something similar will occur for you and "Blonde on Blonde".
By the way, which company's pressing did you buy, and what do you think of the sound quality? Is it good to your ears? I am still considering whether to buy some modern mono pressings of Dylan, and would appreciate some more opinions on those.
My personal opinion of Dylan's best: "Blood on the Tracks" and "New Morning". Give those a try if you want some good "third period" Dylan.