You should use the spoiler tag when you put details about the show in there. It's only decent towards those who haven't seen the last episodes yet.

The way I see it, the mothership was being reconstructed into something else, with human metals. When the ship first arrived, it was probably very invincible to human weaponry because it was all alien metal. And at the end of the season, the mothership has been rebuilt and expanded with human metals - meanwhile, the weaponry used by the humans have increased in power to the point where it can cause significant damage to one of the fighters. For all we know, this could be the first enemy fighter to ever get destroyed. And, for all we know, they each carry a nuclear reactor onboard. Or maybe they just got very lucky and it hit a "power transference wire" or something.

Anyway. Beginning of show: alien metal ship versus human explosives. End of show: human metal ship versus alien explosives.

Heavenfall, I see it a little differently, though I agree with the way it's progressing.

From what we've seen the last two episodes, the tall aliens, apparently the ones who are in charge, don't get their hands dirty. The get their skitters and mechs to do it all. The skitters, we learned, have been harnessed themselves. Wait for the upcoming "big twist" in which we learn that the skitters weren't always skitters. The harnesses remade them, and we're seeing, through Ben, that the human children who have been harnessed are physically changing too. They may end up as skitters themselves, or something else, but in either case they will become loyal drones themselves.

If we work this back, I'm willing to bet that these tall aliens move from planet to planet, wipe out organized resistance, and harness the young to expand their stock of thralls. Using local materials, they construct, perhaps, additional ships to house the new thralls, and then move on to the next planet, or perhaps split up and head different directions to spread like a plague.

Was it stated somewhere during the show, that the alien structure is the Mothership? Personally i thought so originally, but now, given the fact its built from human materials, i am more inclined to believe, its supposed to be some kind of starport or something else...but not the alien ship.

The mothership is the "T" structure.