This has a pretty good summary of the behind the scenes negotiations.
Nine settles WA regional blackout on election night
Says that originally Nine wanted a " guaranteed an amount of revenue that reflected its audience share." rather than the usual affiliation fee that is a percentage of revenue.
Additionally “Regional free-to-air executives believe they have been bullied into paying unsustainable fees for content by metro networks, primarily due to outdated regulation.”
Eventually
WDT had kicked off talks with alternative content providers and was determined to conclude a deal that weekend. WDT gave Nine a Saturday night deadline before advancing talks with other providers.
It is understood the parties agreed to a straight affiliate fee of about 20 per cent of revenues for two years, with no guaranteed share of the market." which is what Prime and WIN had originally offered.