I think they start to back themselves into a corner. The stories they are ALREADY telling start to make it ridiculous that W-Y isn't, not just AWARE of the Alien, but we already know you can find stuff on 3 separate planet/oids that W-Y knows of, before Aliens, in the timeline. At a certain point, they have to realize, you can only keep killing off everyone who knows about these creatures, or has any link to them, so many times, before it stretches logic that it doesn't cause problems for a lot of people. If you ask me PROMETHEUS already stretched it to it's maximum.
I hope they've got some ideas written down for a long term scenario, where both the Company is included in a storyline that makes sense out of how this has all been handled and also maybe does a number on the details they understand. For instance, maybe something happens by the end of the last PREQUEL where the company has misunderstood or mistaken the discoveries and events with the Aliens, in such a way where they know there is an 'ORGANISM' of sorts but don't quite understand what they are dealing with?
Personally, I think filling any more planets and chapters of this story up with new colonies, and regular joes who all die and obliterate giant ships and colonies, before the company can find out about the Alien, is both tired and not progressive to the series. I also think it can potentially cheapen the original franchise. I dunno. I guess I think the approach should be subtle and contained, but I also want to see more of the Company's side of things.
Actually, a story about an INVESTIGATION into the company cover up could be interesting. This is why I liked the idea of Amanda in Isolation. It makes sense to investigate your mother's disappearance. The key to new story ideas is always the characters. What kind of people would need to be included in this story for ALIEN to make sense? Then pick the most interesting roles. Maybe like a Film Noir Alien film could be cool. Or even something like OUTLAND. Something really LEFT-FIELD with the Goo like a synthesized drug or technology, that side-tracks away from the Alien... They need new ideas.