The biggest problem they face is the Playstation 3 (Which has approximatley 512MB of RAM to work with (256MB System / 256MB GPU), that's not a lot of texture/model data on top of everything else the game has to cope with.
This drastically reduces the amount the size that each area can be (without a little technical adjustment).
There are options such as more aggressive performance counter measures such as; shorter draw distance/procedural loading methods, but for their current setup a procedural area loading system would be VERY difficult with their limited memory real estate. (If you've used a PS3 you'd already know it's pushing the limit on performance saving methods to the point where the game is barely even there)
As a result of this hardware restriction, making wider areas would mean sparser design/detail to the world which is something the development team wanted to avoid. They wanted a balance between world composition/detail and map-size, so until support for the Playtstation 3 is dropped this map size restriction and design is likely to stay in it's current form.
I completley agree that Aethertyes are all too common in ARR, they've in-turn made the world feel even smaller, albeit convenient.
Fatigue systems have been known to cause a lot of problems in the past, they'll be avoiding this. As maps won't be getting any bigger than they are currently, things like this simply wouldn't be needed as complex, large and heavily detailed areas simply won't be possible (See above).
Tornados/Meteor Showers/Tsunami's would cause a huge world-impact and some massive changes to the world around you, it's unlikely we'll see this happening in general areas, as the development time to adjust assets to suit this would be insane.
HOWEVER! For new maps as you said, there may be specific weather they'll add in for certain places that could trigger weather events or dangerous conditions to make certain enemies/FATEs/nodes (whatever) appear, we'll just have to wait and see.
Again, the skyboxes take a lot of time to perfect, adding in more of these would be an un-nessecary time consumption but we might see new ones for the areas in the game (as you may have already noticed certain areas have different skyboxes to suit).
"What the hell is a skybox?"
Essentially it's the trick used to make the sky you see, where either a box or a dome/sphere is used to create the upper atmosphere and horizon you see using a neat low-performance impact trick;
https://developer.valvesoftware.com/wiki/Sky_List
http://www.realityisagame.com/archiv...t-is-a-skybox/