We want to implement a multi-seller, affiliate-like shop but I'm stuck at which module to proceed with. What exactly is the difference between the two? Documentation is quite general and one can not tell which one is better.
Ubercart Marketplace is where you want your "sellers to post their products" - more like eBay.
Whereas Ubercart Affiliate module is where "you sell your products" but affiliates help marketing those by spreading your site's links. This is much like the affiliate programs that are run by most hosting providers.
This is the primary difference. And they both plug to Ubercart. So they can leverage all UC features.
However it is possible that you use both in conjunction. Never tried that out. Would be interesting.