The Solar system is a very big place and Pluto is 100 times further away from the Sun than Mercury. The Orrery draws the orbits of the planets to scale, so if Pluto is shown, then all the inner planets would be squeezed together in the middle. You can change which planets you want to see using the Field of View button.
Remember, although the sizes of the orbits of the planets are to scale, the planets themselves are not.
The Electric Orrery positions the planets by calculating the orbits. Since Pluto was only discovered in 1930, and it takes nearly 250 years to orbit the Sun, we cannot calculate its orbit very accurately far into the future or past. Therefore, the Orrery only calculates for about 100 years into the past and future.
As explained above, we are not sure about the exact orbit of Pluto before about 1900 or after about 2100, so only the 200 years of the orbit between these points is shown.
The shadows are, of course, not real. They are there to show how some of the planets move up and down through their orbit - they don't all stay exactly on the same flat "plane". Try watching Saturn go round on the Visible Solar System view.
The fast animation mode steps forward or backwards one year at a time. Since the Earth takes one year to orbit, it will appear not to move. Why do you think it "wobbles" slightly?