I would imagine there are more than just technical issues. Cedar Fair and Six Flags have fundamentally different pass structures and benefits. Moreover, Six Flags, itself, has several different pass and membership options, none of which seem to resemble each other at all. Integrating them is bound to be a colossal mess. And there are going to be a lot of people who are going to lose benefits and accesses, who will be very upset. So, there has to be a strong information and marketing campaign, as well.
For example, I know that in my case I have Six Flags' Diamond Elite VIP, because I paid throughout COVID, and a Cedar Fair Prestige Pass with an All-Parks Passport. I have the All-Park dining for CF, but rely on my 50% discount at Six Flags (which was more effective than a meal plan). SF gives me free The Flash passes every trip; CF doesn't give anyone free FastLane ever. SF doesn't even offer the membership I have anymore. So, what will I lose, when the systems are merged? How would access to all of the parks compare to what I am paying right now for a SF membership that was upgraded for free, because of COVID? What does any of this mean for my meal and drinks plans? For my food and merch discounts? For my other benefits?
All of this to say that I actually don't understand why they are even planning to merge the systems before 2026.