So each owner gets a team consisting of say 1 QB, 2 RB, 3 WR, 1 TE, 1 K and 1 DEF (plus a bench) from the AFC and one separate team from the NFC? And I could trade, say, Kaepernick for Forte but I could not trade Forte for any AFC player?
I think it's intriguing. Have you thought about which site you'd use to run this league and confirmed that it has the functionality you need? I'm not sure how the draft would be run, for example, with each owner picking two teams. And you'd want to set the schedule so that each owner's AFC team and NFC team don't play each other, etc.
If I were commish I'd probably set the entry fee for Year 1 pretty low and call it a beta, and then up the stakes in Year 2 once you know you've got something that works and have had a season to work through whatever kooky situations arise.
I vote "cool concept". Post back sometime letting us know if you decide to do it.