I know there were problems trying to navigate to different URLs in 2013, even from within an IFrame, I believe due to some "black magic" implemented to try keep you within the same window. I'm unsure if there is a hotfix or update rollup scheduled to fix
this.
Let me ask this first though, when you say you want to open different "entity views" do you mean open up a form (i.e. 1 record) or do you mean a grid view (i.e. a list of records)? The reason I ask is the former is much easier to obtain using the the Xrm.Utility.openEntityForm
(see here: http://msdn.microsoft.com/en-us/library/jj602956.aspx). I'm not sure how you would achieve the latter though.