Looking back, Shigeru Miyamoto considers that the main failing of the project.
"Well, when we first initiated talks about a Super Mario Bros. movie, I tried to emphasize the point that the Mario Bros. games are fun as videogames and if we were going to make a Mario Bros. movie, that movie should be entertaining as a movie, and not a translation of the videogame," he told Next Generation. "I think that they tried very hard and in the end it was a very fun project that they put a lot of effort into. The one thing that I still have some regrets about is that the movie may have tried to get a little too close to what the Mario Bros. videogames were. And in that sense, it became a movie that was about a videogame, rather than being an entertaining movie in and of itself."
Meanwhile, I posted this earlier about his views on the '93 movie.
Interesting criticism of what he saw the flaw to be when compared to what they are now making.