In the Koopa chair scene

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Actually I think you have a valid point. The only thing that I noticed was different about Koopa after going into the machine was that he was displaying some odd reptilian traits (the close up of his eye, his snake-tongue in the scene with Daisy and his forehead morphing) but nothing substantial. It's a real shame because I was really waiting him to turn into a dinosaur and try to squash the Mario Brothers or something.

I guess the directors had some sort of an idea early one about the scene but for whatever reason didn't come through with it, which is really sad since now that scene is just amongst the many in the film that didn't really make whole lot of sense.

I think because it aborted for whatever reason. Mario and Luigi had no idea how to work it, and it just automatically switched off after a minute I think.

I think it was because the setting was not low enough for him to be turned into slime...