Interesting topic. Amazon vs Clickbank. I had the same dilemma a while back. I ended up with using neither waiting on the implementation of ShareaSale, without being enthusiastic. It just so ended up being the best alternative with my backend provider FastSpring. These are some of the problems I ran into:
They want a large piece of the pie. At least 30%. Secondly they ideally want to the book on your site exclusively. Thirdly you are not able to build up the value of the book by adding bonuses or other value adders. More to the point, you have less flexibility to create an offer that increases perceived value. However, given their monster position in the market they will probably take over the sale of most ebooks, forcing those who want to make more than $10-15 pr copy to redo their business model. If you go there you are basically a little fish in the water.
Crap interface, and they mess with what you can have on your sales page because they are so tickly with their 60 day money back guarantee. However, they have the largest network, so most internet marketers use it. That being said, do you want to be associated with being a "clickbank" product. They also don't offer any social media integration in the back-end.
I ended up with using FastSpring in the backend for my sites. Not a happy choice since it reduced the alternatives for affiliate program integration.
If your only two options are those two I would suggest just focusing on answering one question; With my type of product and business model, which site will I make the most money on?
Look up competitors on Amazon and look at their rank. It is an indication of sales. Google how that is the case. Then compare against competitors on Clickbank.