I'm going to assume you never played Metroid Fusion.

The short version is:
There's this flying slime creatures that are super parasites called "X Parasite" that can enter your body, copy your memory + genetic information, kills you and then can take your form and mind.
This creatures were in a space station and manage to kill everyone.
And Samus was in charge to solve this problem.
There's also this creatures called "Metroid" that are the natural predator of the X parasite.
The image above theory is that the X parasite were able to come up with a plan to kill the metroid + Samus + getting out of the space station. Proofing that the X were super intelegent creatures capable of long term planning.

That's what it means.

"Samus was only a secondary threat at best pretty much all that time."

Well. One single SA-X was more then capable to win in a 1v1 against Samus for 95% of the game. So you're not wrong about that.