Though at the moment, NPC Designer does not have the depth PCGen has to choose from in the way of monster selection at this time, we are moving quickly to change that. What NPC Designer does do that no other system does is focus solely on the creation of NPCs with clear and detailed stat blocks. Most of the system is exposed to the users so if they wish to apply house rules, changes or alter things it is completely within their grasp. Development is pretty much user driven at this time, people tell me what they want to see or features they need for their game and usually in a few days it is available for them. We started with the primary races and such found in the SRD and have now been extending the functionality into monsters, to that we have just finished the functionality for handling Monsters without classes, Advancing Monsters and Monsters with natural spell casting abilities (like dragons and rakshasa).
Can't say it is better then anything because products like PCGen have a great amount of maturity behind them however I can say NPC Designer is moving in the right direction to be the premier tool for NPC Generation. If you have any specific questions feel free to ask.
