The reason why people really don't like guys altering Rippetoe's novice program is because the target audience of this program doesn't know anywhere near enough about training to make appropriate adjustments. You'll see newbs who are 135 lbs complaining about their "bicept peaks", and they want to train their upper-inner chest because it's a weak point. This is laughable simply because their entire body is one big weak link! In reality, they aren't really weak, they are simply untrained.
The flip side is that anyone who actually needs any type of specialized instruction is already well-trained and conditioned, and they have identified true weak points...well, they shouldn't be using this program's template! They have specific needs that require addressing. The novice's only "specific need" is to get bigger and stronger overall. The target audience is not someone who actually has weak points, the target audience is someone who hasn't been training long enough to know what a true weak point is.
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The reasons against deviation from this program are very logical - an untrained guy is untrained, he is one big weak point. He won't know what his true weak point is until he has spent many months (and possibly even a few years) training and learning how his body responds to overall training. Is his upper chest REALLY a weakpoint? Yeah, his upper chest is a weakpoint because his entire chest is weak! He needs to spend time training his chest with the basic pectoral developing exercises before he decides to specialize in incline DB flies and cable crosses and reverse pec dec inverted flyswatters.
Does he honestly have a "poor biceps peak"? Definitely! He honestly has a very poor biceps peak, and that is easy to understand because he is a buck thirty, soaking wet, with 14" arms. Yup, his biceps peak definitely sucks!
Honestly, how can one know anything about training if they themselves are untrained. They have no experience, no point of comparison, no idea of what truly works because they simply haven't experienced training themselves. You can read a science book and learn that a shark is in a specific genus/species. That is knowledge and is easily applied, because it is based on factual science. Training is NOT factual science, it is an artform with a VAGUE and unproofed background in science.
How would an automotive engineer take the advice of a 13-year old who had never driven? The 13-year old is convinced he knows the best way to design a transmission so that it shifts smoothly because he reads Motor Trend each month, yet the 13-year old has driven nothing more challenging than his grandfather's golf cart. As a general rule, a woman will be resistant to taking the advice of a man when it comes time to dealing with the emotional events that occur during "that time of the month", for reasons that should be quite obvious. Are we seeing the connection here?
While the "don't mess with the program!" attitude is dogmatic, and "everyone responds differently because we're all individuals, blahblahblah", the idea of sticking with the program for its intended audience is, in fact, logical and in 99% of the cases it is doing the perspective trainee a favor. Just about every single person who wanted to change the program but didn't has been very very happy they stuck with it. The ones that seem to complain are the ones that have tried to change it to the point that it bears little resemblance to the original program.
Now, since 90% of the people that come to bb.com are novices, Rippetoe's program gets recommended a lot because it's good, it drives home proper understanding and fundamentals, gets them started on the right foot, they learn what is important in programming, and it provides a plan as to how to execute and how to adjust the weights on a session to session basis. Truly, this is really the key to all successful programs even though this information is totally absent or for most people on BBing sites and in magazines.
Ripp's way certainly isn't the only way but it's a damn good method that is as good as any. It is simple, it works, it provides an ideal foundation, and it SHOULD be easy to follow.