As I see it there are three options:
1) There are 18 teams, easiest way to divide this is by 3. 3 conferences of 6. South Africa, Australia + Sunwolves, New Zealand + Jaguares. Simplest option.
2) Reduction of teams to 16 or 15 (take away 1 or 2 Australian teams and 1 South African team). If its 15 teams then 3 conferences of 5, New Zealand, South Africa and Australia + Sunwolves and Jaguares.
3) Has the current format of Super Rugby served its purpose. Its said that Australia doesn't have the numbers to support 5 Super Rugby Teams but how can players develop if not exposed to the highest level of competition. A big reason that people are so down on Australian rugby is because we aren't competing with the Kiwi teams.
Super Rugby becomes a Champions League/European Rugby Champions Cup type competition with the top four teams from the domestic competitions in Australia, New Zealand and South Africa, the top two from a South American domestic competition, the top team in the Top League in Japan and the top team in a Pacific Islands competition. Teams are placed in different pots:
Pot 1 would be the winner of the National Provincial Premiership ie. Mitre 10 Cup (NPP), the National Rugby Championship (NRC), the Currie Cup (CC) and the South American Rugby Premiership (SARP).
Pot 2 would be the winner of the Top League (TL), the runners up in the NPC, NRC and CC.
Pot 3 would be the winner of the Pacific Islands Rugby Premiership (PIRP), the 3rd placed teams in the NPC, NRC and CC.
Pot 4 would be the runner up of the SARP and the fourth placed teams in the NPC, NRC and CC.
No pool can have 2 teams from the same country. Local derbies occur through the domestic competitions and then teams test themselves against the best of the other domestic competitions. Part of the fun of Super Rugby was seeing Australia teams playing teams from a mix of the other nations, not consistently just Australian and Kiwi teams.
Super Rugby weekends could then be held as independent weekends throughout the domestic season as occurs with the European Rugby Champions Cup. The winner of Super Rugby could then play the winner of the European Rugby Champions Cup to determine the best club team in the world.
The current Super Rugby teams could be merged with the local teams from their city. I.e. the Crusaders and Canterbury Rugby would again become the Canterbury Crusaders, the Lions and the Golden Lions would remain the Golden Lions, and the Reds and Brisbane City would merge to become the Brisbane Reds.
The domestic competitions would be:
South Africa
Currie Cup
Blue Bulls - Pretoria
Boland Cavaliers - Wellington
Border Bulldogs - East London
Eastern Province/Southern Kings - Port Elizabeth
Falcons - Kempton Park
Free State Cheetahs - Bloemfontein
Golden Lions - Johannesburg
Griffons - Welkom
Griquas - Kimberley
Leopards - Potchefstroom
Pumas - Nelspruit
Sharks - Durban
SWD Eagles - George
Western Province Stormers - Cape Town
New Zealand
Mitre 10 Cup/National Provincial Premiership Division
Auckland Blues - Auckland, Auckland
Canterbury Crusaders - Christchurch, Canterbury
Counties Manukau Steelers - Pukekohe, Auckland
North Harbour - Auckland, Auckland
Otago Highlanders - Dunedin, Otago
Taranaki Bulls - New Plymouth, Taranaki
Wellington Hurricanes - Wellington, Wellington
Waikato Chiefs - Hamilton, Waikato
Championship Division
Bay of Plenty Steamers - Mount Maunganui, Bay of Plenty Tauranga
Hawke's Bay Magpies - Napier, Hawke's Bay
Manawatu Turbos - Palmerston North, Manawatu-Whanganui
Northland Taniwha - Whangarei, Northland
Rotorua - Rotorua, Bay of Plenty
Southland Stags - Invercargill, Southland
Tasman Makos - Nelson, Nelson
Wanganui Butchers - Whanganui, Manawatu-Wanganui
Australia
National Rugby Premiership:
Adelaide Falcons
Brisbane Reds/Tornadoes*
Canberra Brumbies
Gold Coast Aces
Melbourne Rebels
Sydney Waratahs/Stars*
Western Force
Western Sydney Rams
*Brisbane and Sydney could also have different nicknames with the Reds and the Waratahs kept as state of origin representative teams playing each year.
Championship:
Central Coast Rays - Gosford
Darwin Mosquitoes - Darwin
Geelong - Geelong
NSW Country Cockatoos - Newcastle
QLD Country Heelers - Townsville
South Sydney - South Sydney
Tassie Jack Jumpers - Hobart/Launceston
West Brisbane - West Brisbane
Japan
Top League
Canon Eagles - Machida, Tokyo, Kantō
Coca-Cola Red Sparks - Fukuoka, Kyushu
Honda Heat - Suzuka, Mie
Kintetsu Liners - Higashiosaka, Osaka, Kansai
Kobe Steel Kobelco Steelers - Kobe, Kansai
Kubota Spears - Abiko, Chiba, Kantō
Munakata Sanix Blues - Munakata, Fukuoka, Kyushu
NEC Green Rockets - Abiko, Chiba, Kantō
NTT Shining Arcs - Chiba, Chiba, Kantō
Panasonic Wild Knights - Ota, Gunma, Kantō
Ricoh Black Rams - Tokyo, Kantō
Suntory Sungoliath - Fuchū, Tokyo, Kantō
Toshiba Brave Lupus - Fuchū, Tokyo, Kantō
Toyota Industries Shuttles - Aichi, Mizuho
Toyota Verblitz - Toyota, Aichi, Tokai
Yamaha Júbilo - Iwata, Shizuoka, Tokai
South America
South American Rugby Premiership
Buenos Aires Jaguares, Argentina
Cordoba, Argentina
Mendoza, Argentina
Montevideo, Uruguay
La Plata, Argentina
Rosario, Argentina
Sante Fe, Argentina
Sau Paulo, Brazil
Pacific Islands
Pacific Islands Rugby Premiership
Nadi
New Caledonia
Papua New Guinea
Samoa
Suva
Tonga
There is also the potential that there could be a secondary competition such as the European Rugby Challenge Cup.