My company has always used Commission Factory (Junction) and Rakuten. I always found Rakuten was harder to use and lacked some of the features CF has. Also it seems like affiliates are on all channels so there really isn't a need for two.
I decided to terminate my contract with Rakuten, which had been signed nearly 10 years prior. They said I would have to pay the fees for 7 months as the contract automatically renews every year, this seems unfair and just gave me a very bad impression of them.