I think it depends on the situation. If you can heavily defend one critcal warp point that will effectively block access to several systems, then it is much more efficent obviously to defend the warp point.
On the other hand if you have a system with as many warp points as planets it makes more sense to defend the planets. Especially considering usually one of the planets is much more valuable than the others.
Regardless I think bases are generally a poor choice for warp point defense. It just takes too much micromanagment to get them there, and then they cannot be moved with the ebb and flow of your borders. Those 6 or 8 starbases are great, but when that system is four jumps away from the nearest contested system, they aren't much use. And they are too easily bypassed by stellar manipulation.
It's trite I know, but in the end, the best defense is always a good offense.
Geoschmo