You need to run the DOOM2.WAD through ZWADCONV and use that as your IWAD. This will enable "hexen" format support. No new BOOM/ZDOOM sector and linedef flags are available though.
Look at either ZETH or DeePsea to see what I'm talking about. Neither of these have to have ZWADCONVerted IWADs, but you will be happier if you do:)