I don't know who is claiming that the SSD is the only thing that matters.
Flops are a measurement of one aspect of the GPU. There are a lot of other aspects like ROPs, VRAM (on PC), and these don't necessarily scale with Flops. And these aren't even necessarily very telling. Mostly dependent on architectures.
I think it's better to think of bottlenecks in terms of applications instead of systems. Or in a different way of saying that is that there usually isn't a "bottleneck" in a system. There is a bottleneck for an application. For example a CPU intensive game can be bottlenecked by the CPU on the same hardware that another game finds the GPU to be a bottleneck. Like Skyrim on the PS3 was early on largely bottlenecked by the RAM, another game like Uncharted probably tended to find the GPU as the bottleneck.
The reality is probably that third party games won't take advantage of the SSD to it's full extent, and they will probably find their applications bottlenecked by the GPU.
First party will probably take full advantage of the SSD, and I'm sure one of them will meet a situation where the GPU and SSD are meeting each other.
None of that means that the SSD was a bad choice. It still offers good benefits even if it doesn't get used to it's full capacity all the time.