This is an excellent review. It looks as though we share much of the same perspective on both of these sites. I would point out, however, that your statement "The interactive features of Many Eyes are wonderful, and would be a major nightmare to code in AJAX or Flash" isn't entirely accurate. It is certainly more accurate regarding AJAX, although many basic visualizations (treemaps, bubble charts, etc.) can be relatively easy to put together.

Flash's capabilities, through Flex, for information visualization are quite impressive and arguably as easy to develop as Java (Flex has some very java-like properties in terms of code construction). For an example take a look at some of the components over at Quietly Scheming (http://www.quietlyscheming.com/blog/). Even without outside developer components Flex has offered basic chart functionality from release. I'm surprised neither of these sites has taken advantage of it, particular because of its rich data-binding. One possibility is, of course, the 'closed' nature of the platform.