If you are starting up a serious affiliate program but lack experience I would most certenly go with MPA3. The support is superb, which is important since you in all cases need support to get started. Remember that the learnign curve is steap for all kinds of advanced software. The Mansion software has prooven to be extremely stable and fast. When you get the hang of it you will find that you'll never lack any kind of functionality. You will allso most certanly see that everything you do inside the menues is really well thougt through in terms of usability and serviceability. The help menues are allso very good and self explaining.
For MAS i would just say.. after you have started to use that you will curse yourself for not getting it before you did.
And last but not least.. The mansion design team rock's the world!!!
http://www.mansionproductions.com/design
So guess in which direction my vote went..