1) "All a muscle does is contract": Yes but the stabilizer muscles don't contract in a machine. Example: Doing military presses with free weights works not only the shoulders but every upper body muscle including the whole core. Even legs are used in holding up the body and extra weight.
2) Financial incentive for Jones is totally relevant. Jones spent thousands of hours building his machines to sell to gyms. Do you think he's going to tell people "my machines aren't as effective as free weights but they are a pretty blue color so pay me thousands for each one." Also, Jones results were never replicated by anyone else. Again, no powerlifter, olympic weight lifter, NFL, NHL or track and field power athlete works exclusively with machines only but there are thousands who use just free weights.
3) Jones was a genius in marketing but not in science. Having a cam that puts stress on the muscle for the full range and eliminating gravity sounds great but has no effect on real athletes. Athletes compete on a mat or field that has gravity and their muscles have to move in all directions including circular motions. Most of Jones's presentations were to medical doctors who knew nothing about working muscles or engineering so he could say anything he wanted and it sounded good to them. He also insulted their intelligence probably because he had an inferiority complex over being the only non doctor in his family and the least educated.
4) As I said before take 2 people (preferably twins), put one on a free weights only routine and the other on a Nautilus only workout routine and who is going to be bigger, stronger and more athletic in the long run? It's not even close. The workout routine Jones's advocated doing full body and no rest between exercises is terrible as well but that's a whole different matter.
The first point, which I referred to earlier in response to another post you made I will address later as it is more involved.
I made it clear that financial success was and is a measure of success of a product or idea. I just wanted to dispute the notion that Jones was motivated primarily by profit. He was already rich and has been involved in a variety of projects throughout his life. Weider was also motivated by profit, and I believe more so than Jones, in promoting his line of equipment, i.e., free weights.
And there are examples of many who use Jones' training principles. Viator, Mentzer, and Yates being the most famous. Of course, nobody follows any program exactly as prescribed but puts there own tweaks into it. Even Jones incorporated the barbell squat in Casey Viator's routine during the Colorado experiment.
And you're right that no great athletes have been produced using machines only but that would be because no athletes trains exclusively on machines only, just like no athletes train exclusively with free weights. Even during the 70s they still had leg curl, leg extension machines, cable rows/pulldowns, seated/standing calf machines, leg press...
Jones was not a marketing genius. Everyone in the iron game knows who Joe Weider is and I have not met anybody under the age of forty that has ever heard of Jones and his development of the Nautilus Machines. He was a very difficult person to deal with and I think this hindered him from becoming even more successful and well know.
He was an extraordinary engineer and extremely intelligent. All the modern machines now being used are based on his basic designs: using cams for variable resistance, full range of motion, muscle isolation.
Now there is one point that you brought up that I can't really dispute but believe simply by faith and intuition. I believe, and it makes sense, that a muscle is better trained throughout its full range, ideally with a resistance that matches it's strength curve. A Nautilus curl seems to me intuitively superior to the barbell or dumbbell curl because of it's variable full range resistance. But does it really matter? Great arms have been built using just barbells and dumbbells. It is impossible to measure any difference in athletic performance when comparing both types of training but I would suspect it really wouldn't make much of a real world difference.
The best practical advantage I can make for the use of machines over free weights for the recreational fitness fanatic is that it is easier and safer. I want someone to be involved in weight training and fitness for their entire lives. Making it more enjoyable will make this more likely. I mean, even I, who has been training for over 45 years straight, sometimes avoid an exercise I was going to do because I didn't want to unload, load, and reload those plates. I just want to stick a pin in and get to it. Sorry, but I'm almost 60 years old now.
