I think this may well be right. A plot in which Totoro gave the girls a magic bean that would save their mother would make it a rather different story. It's a tricky balance, though, because as you say, there is magic in this story. Totoro does give them a packet of seeds, but on the other hand they're ordinary seeds that don't grow overnight like the beanstack (and children and other gardeners will sympathise with Mei's frustration at that fact). But on the third hand, when Totoro intervenes again, that's exactly what they do.

I don't know whether it was the move to the stage, but for me the thrill of discovery (the house, the neigbours, the soot sprites, Totoro) that suffuses the first half of the story was all spent by the second, and what was left seemed rather half-heartedly propelled to the conclusion. The ill mother, whose illness can be turned up and down like a thermostat as the plot requires, seemed more obviously a device - which is no disrespect to the woman who played her, who did what she could with a very static part.