Mulling this as a possibility:
You port one of these programs for a mid title feud over to Smackdown (my preference: IC)
You make Smackdown a new hybrid of NXT and the main roster, and port those champions to the second show. Use Smackdown to then plug NXT on the network the next night, have an occasional crossover, but start building it as more developmental. Maybe a weekly tv main event on NXT from the main roster with the usual squash matches on NXT.
It's not ideal (I'd prefer to have one tag champ and one women's champ). Balor/Joe, Asuka/Bayley and American Alpha can stand with anyone as "Champions."