#2 -- these are FAR too easy in a sim, and real airports in farm country look just like large industrial farms with runway markings that you can't see from a distance. #3 would be dealing with psychokinetic illusions. Sims have some, but they are vastly different. Pilotage just doesn't work in a sim, as the landmarks are totally different. #4 was ATC.
There are some sims available for that, but quality is all over the map. Getting a 10 year old controller that doesn't know what "line up and wait" means is not helpful. Getting a veteran controller but only in LA airspace works best if you train in LA airspace, and doesn't help you with the really important local procedures you need otherwise. But good luck reporting over the cement plant for KSQL (as nearly every approach there does) when your sim doesn't have a cement plant.
Airports in FSX are too easy to spot. They're more realistic in X-Plane, especially at night. For example, at night, you can basically only spot the beacon, unless you're pretty well aligned with the runways, at which point the runway lighting becomes visible. Not all sims are created equal, don't paint with too broad of a brush.
Regarding ATC, same deal. Yes, there are quality issues on some networks, which is why they have such a bad rap with the r/w pilot community, however, a payware ATC network exists specifically to counter that issue, so again, not all ATC simulations are created equal.
Pilotage is absolutely possible in X-Plane using sectional charts. Lakes, rivers, roads, train lines, and changes in topography are all there, providing you with most of what you need to get the job done? Specific landmarks might be missing, but the concept is there, and it ABSOLUTELY builds chart interpretation skills. Bends in roads, curves in lakes, they're all there.
Lastly. to imply that ATC communications aren't useful if they aren't local is off the mark, imo. I used to fly out of SQL, and I know they ask you to report the cement plant. If local references were the ONLY thing tripping up new students, then you'd be right, a simulation with local refs would be of limited use, but I think that premise is patently false. Students commonly have mic fright, completely lock up, have no idea what to say, in what order, and no idea, conceptually, how these transactions take place.
Pattern work? Flight following? Bravo transitions? Class D transitions? Lots of work to be done there, not much of which requires local references to practice those concepts.
Will they need to know local references at their local airports? Sure. But that doesn't meant you can't train without 'em.
A recurring theme with people who aren't fans of flight simulation is a lack of willingness to compromise. Just because something doesn't perfectly replicate all aspects of every single flight doesn't mean it isn't a useful training aid.
Think of the model planes on a stick that are used in ground schools, or any other visual aid. They all have their place. I think the sim is a great compromise when you pick and choose what to use it for. That, and I wouldn't write off entire areas of knowledge (pilotage, ATC, etc) just because there might be some differences. If there's negative transfer, then I agree, that needs to be acknowledged and minimized, but don't throw the baby out with the bathwater, and realize that not all sims and sim-related services are identical.