A thread at WebmasterWorld named What triggers Yahoo to fully index a site? discusses the issues many are having with having their sites fully or even partially indexed. For many who run large dynamic content sites, Yahoo! is having trouble capturing all those pages and its not necessarily due to the crawler barriers (I know first hand).
One member says; "IMO for what its worth, i think the yahoo index is full with not much room for new content."
Of course some sites can be penalized but I don't believe this is the case for many of the sites not indexed by Yahoo! I am curious what the next two to three weeks will bring.