There's a massive gap between the top of the Championship and the bottom without introducing Gateshead/Skolars/S Wales into the mix right now.
I know a lot of people don't like licenses (unless they have "off" in front of them) but I would have a slightly larger, licensed (or at least minimum standards) Championship. Say 13-16 clubs, 24 league games with play-offs. The other clubs would be in a new National division with the new expansion clubs, semi-pro but still subsidised and with less onerous standards. Winners get promoted subject to minimum standards and ability to sustain the higher level. Automatic relegation from Championship for going into admin.
Northern Rail Cup? Straight knockout, include Championship and National League clubs. Or don't have it at all, whatever.