It worked well from 1996 to 2010 when it was Super 12/14. It would have worked well as Super 15 if they had stuck to the same formula; full round robin with the top six on merit playing in the post season (which was the NZRU's proposal).
The ARU wanted a Conference system because they lacked a second tier competition due to the fact that, with a massive dose of short-shortsightedness, they dumped the one they already started,
the ARC .in 2007 SARU also wanted a Conference system, but their reason was to get at least one guaranteed home post season match.
The original idea of the Conference system was that everyone would play the other teams in their own conference twice (one home, one away) and then they would play all of the other ten teams in the other two conferences once, five at home and five away. Unfortunately, SARU threw a spanner in the works because they steadfastly refused to start Super Rugby early enough, and refused to let it run into the beginning of their Currie Cup, which the did not want to move. The result was that we ended up with a half-arsed version of a Conference system in which some teams didn't meet at all.... it was flawed from the outset, and the mechanics of the system we ended up with (reserved post-season spots for Conference winners plus wildcards) was purely down to self-interest from the ARU and SARU. Had SANZAR adopted a proper Conference System, things might have worked a lot better.
Things got even worse when South Africa, in a fit of pork-barrel politics, demanded a sixth team but still refused to compromise on start dates each season, which meant they had to shoehorn the season into an even more complicated Conference System.
They (SANZAR) had a really good competition in Super 12/14. It was functional, credible, fair and easy to understand, but the whole expansion thing has been a completely mismanaged cock-up. IMO, as a competition, it has gone downhill since 2011.