Depends on the type of content. On an information/content site where users are researching how to spend their money (a travel-planning site, for example) affiliate commissions can generate far higher earnings for publishers--and far more revenue for advertisers--than AdSense CPC ads do.
I remember GoogleGuy saying a few times that it's all about the "value add." Also, do you remember when a Dutch SEO blogger leaked a Google "Spam Recognition Guide for Raters" a year or two ago? That document referred to "thin affiliate doorways" that provided "little or no value-added content or service to the user." The document went on to say that a site had the right to try to earn income, and that Google was simply trying to identify sites that did "nothing but act as commission-earning middlemen."
On the Google Search side, the message should be clear: Affiliate links are fine, but affiliate sites are regarded with skepticism.
An AdSense CPA program is likely to result in a flood of "AdSense thin affiliate sites," just as the AdSense CPC program led to a flood of worthless keyword-driven made-for-AdSense sites. This could limit the program's appeal for advertisers who aren't in the e-commerce business, since advertisers who are paying for leads (as opposed to trackable online sales) may encounter the same traffic-quality issues that they do with CPC ads.