My opinion is simple, squat, deadlift, and press using barbells for safety and scalability and rocks, logs, and training partners for the development of broad functional capacity, if you find weight training boring your doing it wrong.
I'm with Rafe. His argument, well put, is essentially my own. To build strength, or increase stamina, the best methods are those which take into account lessons learned from modern science. High-intensity interval training, Tabata and barbell weight training (compound & Olympic lifts) are the best ways to increase the body's abilities. This type of training is also very enjoyable to some people, including me.
Thirdly, injuries are avoided. our bodies were designed to move this way; it's what we should be best at doing. Overuse injuries are almost non-existant, as if you get tired of running, you start climbing or crawling. Completely different movements. Other injuries are also greatly reduced, as the muscles learn to work together. And I'm not just talking about certain arm muscles. When crawling, your arms and legs learn to work together, and so on.
You are making claims. Do you have evidence to back this up? By evidence I mean scientific studies. If not, then these are opinions and you should try to word a bit differently, i.e. "I feel safer doing natural method training because I feel this is how our bodies were designed to move."
If you honestly only care about looking good, continue, but remember you are giving your own training up for other people's attention, rather than your own personal health.
I care about jumping farther, running longer, sprinting faster, doing high intensity parkour longer, jumping higher and being stronger. Those are reasons I weight train. I'm not, nor is anyone here, advocating training in the style of body builders, who train for hypertrophy (muscle growth). What we're talking about is training for strength. If you want to learn more about the difference, check out the stickied threads in the General Fitness board and start reading up on it.
Natural training is fun. I love it. That's why I had a bunch of people stay at my house this weekend and train. Saturday we went to the forest, Sunday we went to the beach. I'm personally bored of urban parkour, to some extent. Every tree is different, every rock is different. I love the challenge of lifting and throwing logs or rocks, as each requires a unique modification of grip.
Fun is great, and yes, a person doing natural method training, or just parkour will be in better shape than someone who does nothing. However, I'm "old" and busy. I'm 29 (not really old, I know) and I work and go to school full time. Time is not something I have enough of to waste. When I'm out doing parkour, I don't want to do bodyweight squats (pointless anyway) or push ups (also pointless), or anything else, but parkour. I've been getting better, largely through skill training. However, it's because I want to get better at parkour that I'm back in the weight room after an absence of several months based on the non-scientific claims of PK Gens. I've tried bodyweight training and miles of QM. I felt stronger when I was lifting bodybuilder style (high reps, short rest between sets, body-part splits, etc.) I
know I'll be stronger than either using the strength training methods developed by a century's worth of research by the worlds strong men. It's fun being strong, it's useful to be strong and I can't wait to hit those longer precisions, higher wall runs and longer haul-ass runs through the forest.