The ranking system isn’t flawed 
It is just that the one-size fits all approach to title fights, now that we’ve reached four world titles, isn’t as good as it was when there was just one or even three belts. The fourth title addition a couple of months back makes the old style of world title fight creation not work.
We will be introducing Mandatory defences very shortly (we are currently coding) and this will change things considerably.
Another thing that makes it too easy is that managers can ask champions for title fights and largely get them accepted without too much hassle. This will change. Mandatory defences/designated mandatory challengers will be one way to challenge for a title. The other will be voluntary defences by champions and these will be in the form of offers from the champion for the manager to respond to. We will be keeping it (mandatory defences aside) for managed fighters who are reigning champions.
We think this will resolve the variety of issues that we are discussing here.