I think the biggest thing is that flattr doesn't address the issues of ads intruding on privacy, nor does it guarantee that your user information isn't being sold as a way of monetization (since it's an add-on to an existing site rather than a content host itself). The one I'm trying to build does the hosting as well so we can guarantee that ads wont be present (at $1 per user per month, there shouldn't be a need for any additional revenue per user to stay running / make a small profit).
The other thing though is flattr doesn't deal with content discovery very well. It doesn't rank content, it simply measures your own. Think of the one I'm working on as a reddit/hn except upvotes distribute a portion of your payment pool, that way we get a quality hierarchy in addition to distributing payments.