Is there any way to put the 2011 topobase and the 2011 ArcGIS plugin into 2012 or 2013? Seems such a shame just to lost all of that functionality.
No, all subscription addons are release specific. Some things, like the ArcGIS provider are in the box with later releases (though still x86 only). Not sure what Topobase functionality you have in mind, but TB more or less became Map 3D Enterprise 2012, and those same tools are part of Map 3D 2013 (which has only one version). In the end, none of that functionality should be lost in the later releases.
So I guess what you are saying is that the GIS plugin only works on rediculously outdated 32 bit systems. I don't think I worked on the enterprise edition of 2012, so I guess that is why I thought it was removed.