The Golden Rule (also known as reciprocity) is flawed - it is imperfect. That doesn't mean it can't be an ok idea but it means it is not the end-all and be-all of moral/ethical guides.
It really only works if your own moral/ethical code is ALREADY fair and desirable by all parties. At best it says that you should expect to receive whatever you dish out, which is hardly transcendent. It also conflicts with 'Turn the other cheek' (which is a much more transcendent ethical concept, but one I rarely see anyone trying to follow unless they are trying to get into a frat).
The positive formulation is the best known:
One should treat others as one would like others to treat oneself
No, no, no. I do not want Christians to treat ME the way they treat each other. I do not want Muslims to treat ME the way they treat each other. I do not want Jewish persons to treat ME the way they treat each other.
I do not want to be subjected to THEIR ideas of good behavior. I want to be treated the way *I* want to be treated, according to MY ideals. At that point, it becomes a negotiation obviously.
And in the negative form (sometimes called the Silver rule):
One should not treat others in ways that one would not like to be treated
This is a little better, but what if I would be happy to be treated in a way you DON'T want to be treated? I like to argue, I have a sharp tongue and I'm happy to use it and I'm happy to have other people do the same to me, it makes me laugh. I don't have a problem with it, but some people do.
Again, it works best as a negotiation.
And combining the two doesn't improve the situation -- in BOTH cases the Golden Rule basically leaves it up to the subjective experience of the actor. This is simply a poor approach to a good moral code.
One can even find a better code in the rather inane (but funny) movie "Bill & Ted's Excellent Adventure" which states: Be Excellent To Each Other (thanks to n8wide for reminding me of that one). It doesn't define what 'excellent' might be but at least hints at being better than just what YOU want done or don't want done.
Emanuel Kant took a crack at correcting these issues with his categorical imperative. I would argue that he failed in part because, for the most part, we do not want people to make real sacrifices for us. Would you want your child to sacrifice his/her own life for you? I wouldn't. But they probably would feel differently. It is our desire to sacrifice for others beyond what others might wish that gives us part of our humanity.
So I feel like the Golden Rule really only HINTS at aspects of our moral/ethical systems that we like to think we possess, but it really doesn't embody much truth in itself.
See also: Limits of the Golden Rule
To put it succinctly, while the "Golden Rule" is a brilliant distillation of our ethical impulses-it is for exactly that reason that it is an abject failure as moral guide as our behavior is only as good as the underlying ethical impulses. One must look to hone and justify those underlying ethical impulses and for that one must look to the consequences of actions.
So what's better than the Golden Rule? Well, I would start with two principles:
Careful observation of the consequences of our actions.
Cooperatively defining the best behaviors we can identify.
Those are important aspects of any ethical system. Perhaps sometime I'll do a longer post specifically on morality but I think many secular authors have already covered it more in-depth than I can in a blog.
Basically, I would treat it as a science.