Also a big fan of both series.

but if they have struggle dealing against a 2000 human civilization rebellion

There is a big caveat to this though, the combine are ridiculously pragmatic, to the point where they use humans to keep humans as slaves. Why specially create enforcers when there is already units that you can augment/brainwash into working for you, who already are well suited for the environment and atmosphere?

So that's what the combine do, they use humans to keep other humans in check. So that revolt of 2000 humans was really only a revolt against other humans. Stories like that are a dime a dozen on earth.

The Combines dosen’t even have shields, the Combine Gunship can be throw away with just three real life rocket launcher and so far we see that’s one of their stronger airship synts units the combine have.

The shields one is a stronger argument, though again I think that might fall in line with the pragmatism of the combine. If all they are facing is humans, it could be the case in the eyes of the combine that putting extra defenses on your armored units is kind of pointless.

So they may very well have that tech, or something even more superior, but they just don't bother wasting the resources on it.

Couple that with the fact that the gunships are themselves organic/enslaved, the combine probably don't mind that the gunships are esentially cannon fodder. They might have the mindset that they can just breed up more.

But destroying a Borg cube? That is a feat even for an advanced civilization, or many of them.

The combine certainly are an advanced civilization. If you take the peripheral writings as cannon, they have at least one Dyson sphere. The tech for that might be beyond the borg, because even the borg's biggest structures are grains of sand in comparison to the size of a dyson sphere.

Size doesn't automatically mean a win, but the engineering required for a dyson sphere is huge. If they have that level of engineering, I could see them taking out pretty much as many cubes as they like. Especially if their dyson sphere(s?) are in any way weapons weaponized. And knowing the combine, they probably have sought such a weapon.

personally I think being a Stalker is worst than being assimilated by the Borg

Agreed 1000%. I'd rather be a borg than a half life stalker. If I'm going to have a hellish life with no agency and only pain, I'd rather not be conscious.

At the end of the day, the true strength of the borg is not particularly well defined (at least in my opinion), and thr true strength of the combine is even worse defined. The writers on either side have left too much up to question for any real definitive answer.