1) Apple® changes the connectivity specifications. There are thousands of people who bought expensive sound systems with iPod docks -- only to have the dock become obsolete when they bought a new iPod.
2) The 30-pin connectors built into the docks are susceptible to breaking. A friend of ours just visited his daughter in her college dorm room. The daughter, her roommate, and three people on the floor all had sound systems with broken connectors.
What we recommend.
Buy a separate iPod dock. The one from Apple is $50 and works very well. If the connector breaks, you can buy a new dock. If the connectivity or charging protocol changes for a new iPod/iPhone model, you can buy a new dock. It's a lot easier and cheaper to buy a new dock than to buy a new sound system.
And that is why we don't build them into our systems.