Getting your body in great shape through physical training certainly helps prepare you for altitude. However, the ability to adjust quickly to the changing oxygen content is largely genetic. As the Kilimanjaro climbing success rates show, some people can climb Kilimanjaro in as little as 5 days (not recommended), while some still fail with 8 days. It is impossible to tell how well a prospective climber may fare in an oxygen deprived atmosphere until he or she is actually in it.
High altitude training systems enable climbers to pre-acclimatize at home, drastically improving the success rate, safety and enjoyment of the climb.
Altitude training systems simulate high altitudes to induce beneficial biological adaptations in the body. Besides going to (and staying in) high altitude places, using a high altitude training system is only way to pre-acclimatize to high altitude before your trip.