In Ben-Hur, JHs job was to play a character, and he did it well.
I really hope that the box-office failure of Ben-Hur does not hurt his career. The film had its issues, but IMO he wasn't one of them.
This time around, the vision of the filmmakers was to have the character portrayed realistically as a human being who undergoes a series of transformations. Their vision of the character had weaknesses, emotions, and flaws.
I think that most people who saw the film, and definitely the reviewers, already had the iconic image of Charlton Heston branded into their minds. He is masculinity personified, as opposed to a warts-and-all kind of guy. This led to some unfair comparisons between the two, where it seems like Huston is being criticized for not being Heston.
IMO, Huston is the anti-Heston. While Heston was a character in and of himself, no matter whom he happened to be playing at the moment, Huston's strength is in disappearing into a role. It's different, but, if anything, more relevant to what people expect from an actor in this day and age.
At the end of the day, you can't criticize an actor for giving the filmmakers what they ask for, and he did that very well. What more can you ask for?