The problem which the organisers face is that there aren't enough quality teams to make a lengthy knock out stage feasable. At the football world cup for instance the last 16 after the group stages, where not that predictable. France and Argentina(a year on its still beautiful writing this) didn't even make it through the group stages. In cricket if you went straight into the quarter finals from the group stage I think its fair to say that the 8 teams would be Aus, SA, Eng, WI, Ind, Pak, SL, and then one of Zim, Ken or possibly Bangladesh(ok I know but it is still 4 years away). this essentially makes the whole group stage thing a little pointless, ie the 1996 world cup. So I think the super six idea, until we have a genuine world game, the best one. The only other way I can imagine they might do it is to have 4 groups of 4 and have the winners go straight through to the semi finals. I suppose a variation could be to have the group winners and 2 best runners-up go through to the super 6, where every team faces each other.
This would then have the added advantage of meaning the majority of games would be between decent sides. The one thing that spoiled the world cup for me(apart from england getting screwed) was watching to many games involving minnow nations. Cricket is a game where it is harder for the total underdog to win. Most other sports, team sports in particular have a greater degree of uncertainty in games involving good teams and minnows than cricket. I know Kenya got to the semi final but they only beat Zimbabwe and Sri Lanka (did that game ever get throughly investigated by the ACU because Sri Lanka seemed to be trying very hard not to win!!)
With 4 teams of 4 it would mean more time initially involving minnows but once they we were into the super sixes the competition would increase. I felt this time round the super sixes were almost devoid of any excitement and it was a huge relief when the semi finals started.