Solutions

1) After repeating the exercise a number of times you will notice that the behavior of the system depends on exactly where you put the planets. The closer you put the planets initially the more strongly they will interact and pull each other out of their original circular orbits. In general however after 100 years you will find a number of the planets have collided, been ejected from the system or put into very far flung orbits (often its the smaller ones that get kicked out). Thus it is likely that you will have fewer planets than you started with and many of the ones which remain will be moving on non-circular orbits.

2) The massive planets ("Jupiters") in the inner solar system do not experience as strong an interaction among themselves as the ones in the outer part of the system. After 50 years the inner 3 big planets will have their orbits slightly modified. The outer Jupiter’s however will pull each other strongly away from their original circular orbits (especially the last two bodies). This occurs because the Sun’s gravitational force becomes weaker in the outer solar system allowing planet-planet interactions to become more dominant in the "mechanics" of the orbital motion.

3) A highly elliptical orbit is bad news for Life. The temperature variations the Earth would experience as it swung closer to the Sun and then farther out in space would make it very difficult for many forms of life (animal life in particular) to survive.

4) For a 600 MHz chip machine 100 years of evolution (with the slider-bar set to very fast) took 100 seconds. A billion years is 10 million times longer than 100 years so it would take 10 million times 100 seconds which equals 1 billion seconds (31 years) to simulate just 1/5 of the lifetime of our solar system. To really "solve" the problem of planetary system evolution then you need advanced (fast) supercomputers and computational techniques.