The answer like to any vs. discussions is "Who ever the writers/editors" want to win.
Sure we can make a pile of super duper powered people on X-men side to argue they will win, but when the writers want the rest of Earth's heros to win they just have Iron Man and his fellow smarty pants make a "screw the X-gene" device, or Doctor Strange puts Earth into a dimension where every super power is "summon a pie" so it comes down to a big cake throwing fight, Galacta appears and threatens to eat everyone if they don't stop trying to destroy earth, or Bruce Banner stands infront of a mirror and says "Jack Kirby" three times at which point the guy appears and scolds everyone involved about how dumb this hero vs. hero fight is and everyone goes home ashamed, etc.
If i recall right the circumstances of Empyre were basicly constructed so Alpha Flight was kept out of the loop about the invasion until much later, which seems to have been simply done so Brand could get angry at Captain Marvel, quit and be free for the allready in planning SWORD series.
So it's less the heros getting beaten by plant aliens and more the writers just creating a quick excuse to free Brand from her obligations towards space Alpha Flight.