I liked the Lara scenes in Superman II better as well, but I also enjoyed seeing the Brando footage.
As has already been said, I think editing could be the factor (did they choose Brando's best takes? Could the shots being edited a bit more tightly?)
For me the problem wasn't Brando so much as REEVE.
If I remember correctly, the Brando-Reeve scenes were the first scenes Reeve filmed for the movie? He comes across as a bit more theatrical, emoting and telegraphing his emotions like crazy, and so it looks like it can be misinterpreted as "bad acting" or "overacting", but I believe his acting style was more "theatrical", which would make sense given that this was his first major film. But it's also the wrong "note" for a film. (He also may have also been trying to match Brando's stature, this being his first (EDIT: major) film role and having to share his first scenes as a major film actor with the greatest film actor of all time.)
However, it's pretty clear that by the time they were filming his scenes with Susannah York, Reeve found his rhythm as a "film actor" as opposed to "theatrical" and his emoting became more "natural" and realistic.
I have a book about film acting where Jack Lemmon talks about his first movie and Lemmon said that the director was telling him, "Less, Jack." "Give me less, Jack." "Less, Jack."
Lemmon said this went on for days with him "acting his head off" and the director telling him, "Less". Finally, Lemmon got frustrated and said, "Are you telling me to not act?!" And the director replied, "Oh, God, yes!"
So I think it's obvious the same can be said with Reeve in the early part of filming Superman.