According to the guidance used by UKVI, the only time an ILR application will be considered when the current visa has expired is in exceptional circumstances. Like bereavement..

I don't think your case falls under any exceptional circumstance. As Rayna says, your wife is now an overstayer with no good reason for it.

You should have started thinking about the ILR at the time of getting the last FLR. I don't understand why you left something so important so late.