It's too bad that an otherwise-okay movie (Jones) and otherwise-really good movie (Panda) were marred by irrationality. I'm not referring to the woo in Jones and the magic in Panda - that stuff just comes down to whether the films have persuaded you to suspend your disbelief.
The problem is that Indiana Jones teaches that too strong a desire for knowledge is part of what motivates some people to be evil, and the desire can be a killer. Panda says that you can do anything if you really really believe it. The motivator in Jones is just trite. Panda too much resembles the neocon Green Lantern theory that all you need to triumph is to will it to be so. I've had enough of that stuff over the last few years.
Still, if you can set that part aside, Kung Fu Panda was really good - just be sure to tell kids and conservatives not to draw any lessons from it.