I'd love to see it happen, but I don't expect it anytime soon. Google and Amazon are joined in the
Internet Association cartel. Considering they are working together behind closed doors, I'm sure they have some sort of "understanding" that ensures they don't turn on each other.
I also believe that rel=canonical was adopted by Google to benefit Amazon. Rather than using noindex on affiliate generated URLs, or disallowing them with robots.txt, Amazon now can use rel=canonical to juice up their own non-affiliate pages. Before Google began supporting canonical and Amazon made the switch, there were far fewer Amazon products sitting in the top spots of Google. Although Google claims to know the major sites that use affiliate links, and allegedly deals with them accordingly, it's pretty clear they are not devaluing the links Amazon is getting from affiliates.
Amazon holds the highest rating of any major e-tailer. They recently spanked WalMart by ten full points in a customer satisfaction survey. That makes it even harder for anyone to negatively judge Amazon. While we know better, and have witnessed bogus reviews used across multiple products, I think Google needs Amazon at this point. If Amazon was flushed out of Google's SERPS, shoppers would quickly learn to visit Amazon first and bypass Google altogether. That would devalue Google's role and importance in product based search queries.
The Internet Association is the greatest threat to small businesses and affiliates. Although their mission statement claims that they are the voice of the internet economy, it's pretty clear that want to dominate this one trillion dollar a year industry by pushing small retailers/affiliates out of the system unless they pay. And these people must pay to either be in Adwords or a hefty percentage of each sale to Amazon if they choose to sell there. Either way, these powerhouses want their cut and will further squeeze small businesses to drive their own profits higher. For a global economy that has produced very little job growth, a forceful shift to a warehouse shopping experience for ordinary goods does not bode well for people that are looking for work.
Also keep in mind that Amazon's volume gives them quite a bit of clout in negotiating shipping rates. The fees that Amazon pays for freight further places small businesses at a competitive disadvantage when they too are selling the same products online. I've seen it happen a number of times personally. My sales were great until the manufacturer decided to sell on Amazon. Once that happened, sales plummeted because there simply was no way that I could compete when Amazon's margins were far greater than mine and their shipping fees far less. This puts small business employees out of work and replaces that with a single Amazon warehouse worker. And people wonder why the economy sucks ass.
I could go on with my rant, but the bottom line is that Google and Amazon are partners in the Internet Association. Knowing how these companies work, and how they both are squeezing retailers and affiliates, I'd say we have a legitimate reason to be concerned for what the future holds.