What kind of information did Weyland-Yutani need/want from Hicks? And why would they only take Hicks for questioning and not Ripley, Newt (the sole survivor of the colony) or Bishop (who is their product)?
The "Stasis Interrupted" DLC answers this, by showing that Hicks was woken up by colonists from the Legato just before the cryopods were ejected.
Prior to the beginning of the game, Weyland-Yutani accesses the Sulaco and all of its cryopods (including Ripley herself), kidnaps Hicks, jettisons the cryopods with an infected Ripley inside, pulls the Sulaco back to LV-426, starts Project Origin (breeding xenomorphs with eggs found in the Derelict) and uses the Sulaco as a test hive. Why, then, do they decide to go back for Ripley in Alien3 when (a) they already have plenty of test subjects on LV-426, (b) a live Queen who they've been experimenting on, and (c) access to plenty of eggs in the Derelict? This makes even less sense in the Movie Map Pack DLC, where you can find W-Y equipment strewn all over the Fury 161 facility that has no discernible purpose.
The "Stasis Interrupted" DLC rewrites/retcons this by stating that two civilians from the Legato - Herc and Stone - woke Hicks up, and that the ensuing fight with a group of W-Y PMC's caused the cryopods to be jettisoned. However, there's still no explanation for why the Sulaco was towed back over LV-426, especially when it's revealed in the same DLC that the Legato was already involved with construction on Project Origin (and even had xenomorph samples) when they were waylaid to rendezvous with the Sulaco.
Why was the Sulaco brought back above LV-426, and why did Weyland-Yutani decide to convert the Sulaco into a xenomorph research lab when it likely isn't equipped or even particularly useful for such an endeavor?
It makes sense, using the ship meant less construction time on the planet, and it could be used to move men and materials to and from LV-426, it would have doubled their transport capacity. No logical person would just let the ship go when they could find a use for it at any time, they could always get rid of it later.
This makes more sense with the arrival of Stasis Interrupted where it's revealed Weyland-Yutani did have a dedicated research vessel which was lost. So the remaining researchers may have just been making use of what they had.
The game is said to take place seventeen weeks after the events of Aliens. Wasn't the period before stated in the movie seventeen days, not weeks?
What are you even talking about? The only mention of that time frame in the film is when everyone is freaking out that a rescue ship wouldn't be coming for them for 17 days.
That's more or less it exactly. The marines in this game are those referred to in the movie as arriving in "17 days." So the timeframe doesn't make much sense.
How did anything survive the explosion of the atmospheric processor? Not only it was very visibly huge and catastrophic, but Bishop himself gives an estimate of the blast's yield ("a blast radius of 30 kilometers; equal to about 40 megatons")
This is actually the MOST believable thing about the story. The atmosphere processor was partly or mostly underground. There were also a lot of hills and mountains. Ground bursts are not very effective for nuclear explosions as they waste a lot of energy. An explosion in a heavily shielded partly underground facility would waste even more. Really destructive nuclear explosions are airbusts, and they are often set off 1km or higher above the ground.
While that's all tecnically true... well, it was a 40mt blast. A ground burs of such yield would demolish everything (even reinforced concrete buildings) at a radius of 7 kilometers and a half. Furthermore, we saw it going off, it was massive. There is simply no way to handwave that the facility survived as anything but memories, much less in a semi-functional manner like in the game.
According to the devs, it was a "vertical explosion". Whatever.
It's the same principal as an RPG, not all explosions are spherical.
In the "Stasis Interrupted" DLC, (a) how does Hicks know where to go to find Michael Weyland during his confrontation with Ripley in the leadworks, and (b) how does he know it's Ripley who's fallen into the molten lead when all he can see is a bald person standing quite a distance away with their back to him?
According to a Wey-Yu scientist, even if a chestburster could be removed surgically, then the cancerous placenta would still kill the host. The problem with this though, is that I think Ripley 8 would beg to differ.
Ripley 8 had alien DNA, remember. She wasn't fully human.
The Dr. Shaw case was not, strictly, a chestburster. It might not have the same side-effects, given the differences in infection and resulting creature (and if one wants to be technical, there's no actual proof Dr. Shaw did not fall ill and perish shortly after Prometheus, so until the sequel comes out...).
Prometheus!chestburster and Alien!chestburster are two totally different species that happen to propagate in a similar fashion, probably due to the fact they were both bioengineered by the Space Jockeys/Engineers.
What was the point of Weyland replacing the lab's defensive nerve gas that was lethal to xenomorphs to a mixture that was only lethal to humans and made xenomorphs sleepy? (And it's seen that it doesn't even affect xenomorphs anyway) Weyland made it abundantly clear that he didn't want his specimens destroyed but if that's the case why replace the gas with something completely useless and potentially obstructive to the scientists and bodyguards rather than just doing away with the gas entirely?
About the ending, aren't the Colonial Marines on the ship at the end completely screwed? They're stuck on an FTL ship that's crawling with loyal We-Yu mercs and scientists and potential xenomorphs as well.
And for that matter, what about the rest of the Marines that took part in the assault?