First of all, we have always thought of the dynamics of parenthood as 'me right, you wrong' and our discipline follows along those lines. But when we take that stance, our lives with our children become an escalating power struggle as the 'little ones' strive to assert themselves as independent entities.
If you need further incentive that an adult independent thinker is what you want to raise, just think of who will be making the decision on your senior care at that point of your life. Do you prefer someone who doesn't know how to make the right choices? someone who doesn't know how to think things through?
I think the answer to that is no.
The first step to raising an independent thinker is to teach them right from wrong. Now this is not an easy thing to do with a young child, but children from an early age can be taught self-control. I used to resort to punishment while raising my children. That seemed to teach them nothing except 'we better not let Mom see us doing this'.
What worked best for me was the following speech:
"You need to control yourself. If you don't control yourself, I will have to control you - and you know you don't like to be controlled by me."
They did not always see it my way initially, so the second part of that speech was waiting in my bag of tricks.
"If I can't control you, I'll call someone who can."
Needless to say, I never had to call. But I knew from the beginning that I had to be willing to do so.
The next step to raising an independent thinker is to make them responsible for their mistakes. That might seem harsh, and it is a really tough thing to do, but it is a necessary step. How many times have you seen a sweet kid make a mistake and take a piece of candy from a store? You will notice that I did not say 'steal' a piece of candy from a store. At the age that this most frequently happens (two or three years old), thievery is not the intent. The intent is most often to eat a piece of candy. The action of hiding their attempt to satisfy an urge is not directed at the 'owner' of the goods, but at their parent or caretaker who would probably say no if they were asked to buy that piece of candy.
If the child is punished but not made to take responsibility for their actions, the next attempt will probably be more successful because now they have a background on the subject that tells them "I'm gonna get punished if I get caught" so their goal becomes not getting caught instead of controlling their urges.
Making the child responsible for their action involves an explanation of what happened (please leave out any reference to 'stealing' at that point). Focus on their lack of self-control in satisfying an urge and involve the owner of the goods. Don't take the blame on yourself ("I thought I had taught him/her better than that!") or subject the child to a situation where they will be put down or called a thief. A straightforward approach works best. If the child can make a decision (do you want water or milk?) and verbalize, they should approach the owner of the goods, say 'I'm sorry' and pay for the candy. Of course the money comes from you. That is where the fun part comes in.
At home (never degrading the child) explain what took place and the amount of money that was involved in taking responsibility for the mistake. Set up an age-appropriate set of tasks that will help him/her earn the money to pay you back. And, pay him/her in money (lots of change) for their work. For a 2 or 3-year-old, it might be taking clothes to the dirty clothes basket or helping with the laundry (also a good opportunity to teach them to fold those washcloths). Let them earn more money than they need to pay you back.
This is also the first step to raising financially responsible kids. I know that they don't have all of the concepts of money and it's worth and it's place in the world, but their is no time like the present to start.
The third step to raising independent thinkers is to praise and reward them for making the right decisions. That goes a lot further than punishing them for making the wrong decisions, though those need to be discussed and your expectations need to be verbalized. Never assume that your children are automatically endowed with the 'good/bad' sense. Bring it down to a game level, if necessary. Play a game where you name an action and they respond with (hitting-incorrect/hugging-correct). You can make it age-related.