Just a comment.
You say 'You deal with affiliate requests' is a disadvantage of an inhouse system...is it? Would you rather rely on a third party to deal with your affiliate requests? Wouldn't you like to keep your finger on the pulse of what your affiliates want and what they ask for?
Yes, it's extra work, but I don't think it's a disadvantage.
Also, just to keep things balanced
- on the other side you say a disadvantage of a network is 'Any affiliate program promotions are on behalf of the network, not your program individually' - when an email is sent to a merchants affiliates within a network promoting something, how is that NOT promoting your program individually?