It's really not that complicated. Bring each fighter to the UFCPI for a weigh in with hydration testing. Use that to set the lowest weight class in which they are allowed to fight. Do this in conjunction with a fight so they aren't tempted to jack their bodies around to game the test. If I am not mistaken, the financial penalties for missing weight are assessed by the commissions, not the UFC. Let the commissions do their jobs, but on your second miss, you are moved up a weight class permanently.
Oh, and one last thing: Don't hand out title shots to those who miss weight. I'm looking at you, Romero and Till.