I really liked the first plan presented. IOC seems to like too... I don't know what interest ($$$, of course) mayor Paes have on Port Area, since he wants to change everything to there.
I'm favourable to send some minor venues to there, for example, to build a multi-event arena in Port Area, that later can be used for shows and events. During the games could host the basketball matches... This would be nice...
Barra is far, ok, but it's a place that can be controled about security, since there are few entrances and the Olympic Village in Barra Cluster IMO is the best choice.