Namibia, Zimbabwe and Kenya were all tied on 10 points (2 wins and 2 bonus points) in the African Qualifying. In the end, it came down to who beat up Madagascar the most. I don't think either of the other 2 would have disgraced themselves had they made it instead.
In the same vein, the Russians were one result from going in ahead of the Uruguayans. And IIRC, there wasn't too much between Uruguay and the other teams in their division prior to their Qualifier against the States.
So, you give another spot to Europe, another to the Americas, and another to Africa, and you're 1 spot away from a 24 team cup. And rather than permanently give the spot to the Pacific or Asia, you make 2 repechage places instead. Throwing numbers out there randomly, you could "permanently" assign the number of spots each region gets. So:
9 to Europe, increasing the allocation by 1, but leaving them out of cross conference qualifying.
3.5 to Africa, increase the allocation by one, plus the 4th ranked team gets a playoff.
1.5 to Asia, no change, but greater chance of 2nd ranked team getting through.
5.5 to Oceania, no change to allocation, but 6th ranked team now gets a playoff.
4.5 to the Americas, split 2.25 and 2.25 across north and south, with the 3rd placed team from each playing off for the cross conference playoff spot.
It'd avoid a number of issues like we're currently pondering (i.e. allocations have only ever been done for non qualified-teams, do any of the Pacific islands miss out), and you'd likely only have 1 team, either an Asian or Oceanic side that was significantly weaker than what the Namibians or Uruguayans have given us this time around. And if the Africa 4 and Americas 5 sides drew Asia 2 and Oceania 6, we may not even have that.