Each site caters to a different target audience:
FounderAcharya.com (this site) is intended primarily for a devotee audience. It will grow to be a leading website on Srila Prabhupada, with a plethora of content, regular updates, authoritative commentary and unique features.
Prabhupada.net is intended primarily for a non-devotee audience. It is a static site providing a very modern and accessible explanation of Srila Prabhupada’s life and teachings.