The structures making up the Dark Ones' home are massive Soul Jars housing the souls of the deadNotice how virtually no ghosts were present on the surface in Metro 2033 when compared to Last Light? This was because the Dark Ones had somehow collected many of them into the massive, coral-like structures that comprise their home, in an attempt to grant them peace. But when Artyom destroyed their home, many of the ghosts drifted back toward their former resting places while others were trapped around the Red Square.
The mushrooms the Metro inhabitants are growing are really magic shroomsThe Metro has just a few hundred inhabitants (because it couldn't sustain more due to lack of space and light to grow enough crops), all the adventures in Metro are just the hallucinations of Artyom. All Metro inhabitants sit around all day in an empty, completely non-mystical metro station, they sometimes go into the (completely non monster-infested) tunnels to foster their mushrooms when they are more sober. Not all of the mushrooms are "magic", of course, most are simply champinions. Artyom is just having a bad trip. Oh, and the pigs don't exist either. Feeding farm animals when supplies are low anyway? Not a chance.
The Moscow Metro is not the last outpost of mankind.It seems odd that the equally deep-sunk Metroes of St Petersburg, Nizhny Novgorod, and Gorky would not also see microcosms of the Moscow conflict. Similarly, the entire world may not be devastated - the vast Russian continuance-of-government stations in Siberia might still be in operation, trying to build enough of a society to ultimately reclaim the shattered Western Russia - the ringing phones in D6 would support this theory.
The "Enlightened" ending is actually Artyom getting Mind Raped by the Dark Ones.At the end of the day, we really don't see any evidence that the Dark Ones desire peace and are any more than monsters apart from the visions, which are sent by the Dark Ones. That hardly makes those visions an objective viewpoint. Also worth noting that in the final visions, they attempt to make Artyom jump off the tower, and only stop their attacks and explicitly sue for peace when Artyom fights off the vision and shoots the Dark One giving it. He has no real reason to believe that they deserve to be spared. The only Dark Ones seen in game are those forcing visions into his head, and it is an unprovoked attack by Dark Ones on Exhibition Station that triggers Artyom's mission in the first place.
Metro 2033/Last Light takes place in the same timeline as The Last of Us.As was pointed out in the WMG page for the latter game, they both begin with a cataclysm of some sort in 2013, and then move forward 20 years to the "present"— the year 2033. As for how the plots are connected, the story about the infection originating in South American crops was a cover— it was actually deliberately engineered by the US military, for use as a first strike weapon against Russia. However, it leaked out somehow and began infecting Americans, culminating in fungus-crazed military personnel launching missiles at Russia, to which the Russians responded in kind. Furthermore, the mystery superweapon used against the Kremlin was actually a payload of cordyceps spores that infected and killed everyone within the radius of Red Square. It was subsequently mutated by exposure to radiation, becoming the sentient Biomass that dwelled in the Kremlin basement and lured Stalkers to their doom with its newly-evolved psychic abilities.
The mutant horde that attacked the Rangers was sent by the Dark Ones.Simple enough, really. The Dark Ones are established as having psychic powers. It's not too much of a stretch that they could use those powers to goad all those watchers and demons to attack right as Artyom, Miller, and the others arrived outside their destination. They're clearly shown trying to stop Artyom from launching the missiles when he reaches the top of the radio tower, but the initial attack was to try and stop them from getting that far to begin with. For the most part, it worked, since it killed/scattered most of the Rangers, but it was only after Artyom got really far up the tower, far away from where any other mutant to get him, that they intervened personally. The chips were down at that point, it was their last ditch effort to save themselves, but the horde was their opening gambit rather than pure chance.
Khan lent his help to Cursed Station in 2033 because he didn't want it to end up like Polyanka.In the first game, it's not really explained why Khan is so invested in helping defend Cursed Station from the Nosalis hordes— yes, there's plain old altruism, but the revelations about Khan's past from the Chronicles Pack in Last Light cast the entire incident in a new light. Notice the simililarities in game play between "Cursed" in 2033 and the Khan DLC mission in Last Light— in both, you are tasked with blowing up the entrances to a station that has been totally overrun by mutants in a last-ditch attempt to keep more from coming through. Now try and imagine that similarity from Khan's point of view— he remembers Polyanka all too clearly, and he's watching the exact same thing unfold at Turgenevskaya/Cursed. The difference this time, though, is that he has both experience and Artyom's help on his side— thus, at least some of the people from Cursed were able to be saved. This also explains why Khan says that the whole thing with the ghosts was "very personal" to him— the ghostly squad in the tunnel, while not his original buddies from Polyanka (which would make no sense, given the geographical distance), are still friends of his who died trying to save Cursed from the fate that befell his own home. To Khan, saving Cursed wasn't just the right thing to do— it was a chance to right a personal wrong and make peace with the past.