hi there!
let me be the 1st to tell you that you will recieve the following answer among many others:
1) it's the instructor not the agency
my take on the PADI thing? i'm padi certified but we don't get very many options here... also it's easy to bash whoever's on top... for better or worse padi's got the business side of diving down pat and many (secretly or otherwise) don't look to kindly on businesses doing good (yes, welcome to the land of free enterprise)
it's also because since padi churns out the largest number of instructors on a regular basis, you also get the largest percentage of inept instruction coming under a padi name (it's a matter of averages and ratios) - this doesn't mean that other agencies don't churn out a dud but statistically you'll meet more padi divers than non-padi divers (generally)
that being said and done do this: LEARN during your course. don't just copy the skill and repeat it until you get an OK... DO IT PROPERLY and learn the WHY and HOW of a skill, UNDERSTAND what you are being taught (physiology, boyle's law, ascent rates, expansion, bouyancy, etc.)
if you don't get something or you're not super-confident about being able to do it in your sleep (like equalizing or finning) then make the instructor go over it w/ you again... it's your life on the tank, not theirs, when you're comfy you dive well
finally after everything, CONTINUE LEARNING... SB's a great place to get a lot of good insights... you'll have to trim some fat and garbage out sometimes or sometimes put some salt, but it's a great place to learn from other agencies and compare and contrast w/ what will make you a better diver
hope this helps
Jag