I think this is not quite correct for what the controversy is. My understanding is that Fukaya wrote a paper with brilliant ideas, no one could understand them

I think this is not quite correct for what the controversy is. My understanding is that Fukaya wrote a paper with brilliant ideas, no one could understand them for sixteen years, and then the controversial part is the brashness with which McDuff and Wehrheim engaged with Fukaya. It seems like most people agree that it was a net good for the field of symplectic geometry, because now other people can employ Fukaya's ideas for other problems because they can hope to understand them, but where people are divided is whether this was the best way to get Fukaya to elaborate them.