People bash PADI because they have the best marketing program and that they have streamlined scuba education to the basics as well as broken the training in to manageable modules. The old, triditional method is one long droning course of everything, and then some.
Also PADI has the best instructor support program and does not tie an instructor to a dive shop as some agencies do. Scuba diving was never an evolution from dive shops, dive shops appeared in support of the growing hobby of scuba diving.
The other agument that PADI charges too much is kind of subjective. The cost of marketing, printing, shipping and wages has gone up so the cost of providing services as professionally and effectively as they do will also increase. The cost of gas has increased since WWII, yet the American public is still driving cars all over the place.
Many of the things stated above apply to all agencies- all the major agencies have streamlined training (some more than others) and have broken down training into manageable modules (although most do not use this word). There are some big differences in standards between agencies that can make a huge difference in how an instructor may teach a course.
Best instructor support program is very debatable- I get excellent support from NAUI - much better than what some of my peers are seeing from PADI and others. NAUI does not tie you to a shop and allows you to use online learning, on line student registration and you can buy into the discount programs just like the shops if you desire.
Cost is a big issue and PADI does tend to be more expensive than other agencies - I have never seen the advantage of this higher price others will argue name recognition is worth the extra cost. I have never seen a problem with students questioning the legitimacy of my training or NAUI and I doubt other agencies have any problem with legitimacy either.