A quibble, but that's not really true, it's specifically stated that the aliens weren't indigenous to that planet, so wiping them out there doesn't mean there weren't any elsewhere.
That's debatable.
From a Watsonian standpoint, yes, the xenomorph isn't native to LV-426, and yes, there could be other xenomorphs out there. However, it's pointed out that humanity has never encountered the xenomorph anywhere else by the events of the film, so to best knoweldge, by the end of Aliens (or Alien 3), the xenomorph is extinct.* If it isn't extinct, then it beholves this hypothetical Alien 3 to explain why.
From a Doylist standpoint, it makes Aliens a waste of time in some regards. A key plot point is stopping the xenomorphs from getting to Earth, so in the next movie...they're on Earth. If your overarching story makes previous events meaningless,** then while that can sometimes work if addressed properly,*** here, I doubt it.
*Yes, I know about the fact that countless xenomorphs were encountered between 2122 and 2179 as per EU material. I have my own gripes with that, but in the context of the films by themselves, there's nothing to suggest that the CAA official is lying.
**Even if you argue that Hicks and Newt dying makes Aliens pointless, that makes only their own character arcs pointless rather than the whole movie. There's nothing in the Alien 3 we got that renders the overall events on LV-426 a waste of time, as the xenomorphs are still wiped out, WY can't weaponize them, etc.
***As I'd argue Alien 3 does, since their deaths are relevant to the tone and Ripley's descent into despair.
Um, could you explain why you think that Covenant is good?
Um, most of the film?
Alright, I'll try and boil that down using the Five Elements of Story, so on that note:
-Plot: Plot is good, like how the mystery steadily unfolds. True, I saw some plot twists coming (e.g. the David reveal at the end), but overall, plot is solid.
-Characters: Characters are mostly good. Sure, there's a lot of background characters, so it doesn't get too special there, but as far as the main characters go, things are very solid. Fassbender does an excellent job in playing both Walter and David, how in-universe, they're the same physical model, whereas Fassbender plays each character distinctly. Daniels is okay - nothing special, but quite likable as a character.
-Storytelling: Covenant's storytelling is extremely solid. From the outset, it sets its pace, and steadily ramps things up. From the outset, there's a sense of unease (the solar storm), which translates into dread (exploration of Planet 4), which follows into horror (the backburster, neomorphs), then back to dread (David and the city), then horror/action as the final sequences play out, a standout being where Daniels has to fight the xenomorph on the landing platform. Really, there's no part of Covenant that drags the film or feels superfluous, and in terms of tone, I've commented that Covenant feels like a middle ground between the horror of Alien and the horror-action of Aliens. It isn't as good as either of them, but it's still a solid work by itself.
-Worldbuilding: This isn't completely perfect, as there's some ambiguities that will likely never be solved - for instance, is Planet 4 the Engineer homeworld, is this a separate branch of the Engineers, or are they a different Engineer creation? But aside from that, things are solid here. From a tech standpoint, I love the technology on display (like something that could concievably exist a hundred years from now), from a biological standpoint, I love the neomorphs and the nightmare fuel that comes from the black goo. We can question the notion of David being the creator of the xenomorphs, and it's dubious how things tie up with the Space Jockey (the implication in Alien was that the eggs had been there for ages, and had possibly been created by the mala'kak, though it's also implied in Prometheus that the xenomorphs already existed in some form before said film). The worldbuilding isn't perfect, but overall, it's a net positive.
-Themes: I'm going to address this below, since Covenant builds off the themes of Prometheus. So on that note:
Also, what high concepts that Prometheus was trying to go for, IMHO it's the normal Chariots of the Gods stuff mixed with At the Mountains of Madness, plus added waffle.
-Origins of life
-The nature of exploration - is this a noble endeavour, or are we stumbling into places that we don't belong?
-Deification - what happens when God (or gods) detest you? How does one deal with being a failed creation?
-Tension between science and belief? Can they be reconciled? Again, the different perspectives of David (cold, hard science), Weyland (blind faith/belief/hope), and Shaw (the middle ground).
-Creation - what happens when creators create, who create in turn? Do their offspring surpass them? Can they? Is there degradation involved - Engineers created humans, humans create synthetics, synthetics create xenomorphs - each creation is more malignant than its predecessor. This isn't evne subtle in Covenant, Paradise Lost is referenced directly. There's the running theme that the created can never match their creators, and the associated tragedy involved with it.
You can point out, correctly, that these themes have been explored elsewhere, and explored better. Doesn't change the fact that the ideas/concepts/themes are there. Prometheus has plenty of ambition, and while it didn't work well (to put it mildly), I appreciate Prometheus conceptually. Similarly, while Covenant is less lofty in its ambitions, it does a better job of exploring these ideas.
This also brings us back full circle. What themes, if any, is AvP exploring? I'm not even saying it has to, but when I go to see an Alien film, I expect something more than action schlock.