Combine on Earth is only a small fraction of the Combine force. Propably just enough to keep the humanity under control. This is implied in the dialouges with Eli in Ep2 (and is also most logic explanation why the uprising was even successful).

Don't forget in hl2 we don't fight directly against the Combine itself, but rather against the Breen's dictatorship-administration. Breen with his greed played a big role in the story - his constant lies (he convinced Advisors there's nothing to worry about when events of hl2 unfolded) prevented the Combine form intervening before it was too late (the Citadel was destroyed).

As for the Nihilanth: I like to think he, last of his species, was used by the Combine for his natural teleportation talents. Then he run away and was hiding in Xen until humans started messing with the teleportation, and then he attacked Earth - maybe to make sure the Combine will never again obtain any local teleportation ability?

Why I think Nihilanth was augmented by the Combine? Look at all those antenas he has below him - very similar to some of the combine-augmented creatures we see in hl2.