Re: preserving knees and shoulders....
Free weights and machines both have their roles to play in any fitness program, imho. Machines are great for beginners because the guidance they provide helps to keep the beginner in a more correct form, thus reducing the chance for injury. Once initial gains are made and the beginner starts to gain a feel for the correct motion, progression should be made (under supervision of a trainer or experienced lifter) to free weights. free weights require more balance and coordination, and work the minor joint stabilizing muscles as well as the major groups. It is those stabilizing muscles that protect the join in other sports, like aikido. Still, machines can continue to play a part by providing a safe venue for faster gains, as well as offering certain exercises which are more advanced or difficult to replicate with free weights. They also offer a safer alternative to those who are rehabilitating an injury - in my case giving me an alternative to squats.
Any good martial arts fitness program will use a variety of techniques...which is really true of any sport. Protective and performance benefits can also be seen with the incorporation of other activities like yoga, pilates, plyometrics, and cardio activities like cycling. Consistently changing the challenges you present to your body will give you a better all-around fitness level and help prevent those most annoying plateaus all athletes face.