Honestly, if Ubuntu dropped their ridiculous, underdeveloped, undersupported Ubuntu One services and partnered with Amazon to integrate theirs (Cloud Player/Cloud Drive/etc), that would be a MAJOR improvement for both them and the end-user. Excellent cross-platform cloud services and marketplaces integrated with the OS would be great for bringing less-technical users to the platform in the wake of the proposed "Windo…
An affiliate deal seems to make a much lighter impact to Ubuntu's ability to make independent decisions, in part because the revenue stream is less and also because the service is somewhat fungible–Ubuntu can switch to another online retailer (or suite of retailers).
Also, the perceived switching costs for a consumer to convert from Ubuntu One to Cloud Drive is going to be a helluva lot higher than `sudo apt-get remove unity-lens-shopping` (unless they make ubuntu-desktop a dependent package, making apt return a scary message)