My view on this has evolved to basically one smaller concern that impacts manufactures and by extension mostly us coaster nerds. Think about the last decade or so, (not going to worry about an exact window) and compare what coasters Six Flags and Cedar Fair have purchased for their parks. Cedar Fair has, for the most part, gone with the tried and true big manufacturers and their established, proven models. Six Flags has been much more willing, for the most part, to play around with the cheaper and more experimental upstarts. Six Flags may have been moving away from this anyway prior to the merger, but whether they have or not we have lost the reality of two different companies having the potential of having two different minds as to what type of attractions that they want to build.
The big example is RMC. They probably never get off the ground without the penny pinching Six Flags we have known. The chain also tossed up 4D Free Spins, brought back the compressed air launch, worked with Premier Rides, the new Vekoma boomerang model, etc. How much we like these things individually aside, they were decisions Cedar Fair has been much less likely to make. By extension they are decisions that the new combined company would be unlikely to make had they not already happened. Of course, you can easily flip this too. Six Flags wouldn't have done all these Gigas or worked with the more expensive Mack Rides as obvious examples.
The loss isn't specifically the chances that Six Flags has taken, but that we will have lost an entire independent way of thinking about these decisions. Where there were two corporate minds, there is now one. The coasters going into all our regional parks going forward are going to be much more homogenous in nature. Maybe better overall, maybe worse overall, maybe there will be no overall quality change. Either way, there is likely to be less variety. That is a bummer to me.