I really think the best option (all things considered) is to close off the conferences until the finals, increase the amount of teams in each conference by 3, to 8 each, and promote the conferences within each country as their country's own NPC (i.e. CC, ITM Cup, ARC), all the while maintaining the perception of a single Super Rugby comp. The winner and runner up from each NPC move thru to an international finals system.
There are some good arguments against this of course. There would be no international games during the regular season, and NZ and SA would need to shift the ITM Cup and CC respectively, to earlier in the year.
But in it's favour, the NPC in both SA and NZ would be back on centre stage and act as the premier competition within each country, instead of fans having a conflict of loyalty between Super Rugby and the CC/ITM Cup. And AUS would have a NPC to call it's very own.
Local derbies would be at a maximum interest because they would double as NPC games and as qualifiers for the finals of Super Rugby.
Cross-conference matches would be at maximum interest, no matter what time they're on TV, because they're during the finals, and are more 'mysterious'. People would literally be salivating to see how the best two teams from their country go against the best from the other two countries.
Travel costs and player burnout would decrease without international travel during the regular season.
SA and AUS could better capture their markets, and NZ could potentially reduce costs by supporting only 8 fully professional teams, rather than the 5 professional Super Rugby franchises plus the 14 professional/semi-proffessional provincial teams, it does now.
Player-depth issues for particular countries would be masked with teams only competing within their own conference, and only the best teams playing inter-conferences games during the finals.
If depth is spread evenly with each conference, all teams would find their own conference equally hard to reach the Super Rugby finals.
The length of the Super Rugby season would remain mostly unchanged. The June internationals would then provide a natural break between the Super Rugby conference/NPC games (played before) and the Super Rugby finals (played after).
Every game your team plays during the regular season would be on at an optimal viewing time.