...I'll be honest, I completely forgot about that. Poor Jeremy, now it's gonna look like Izzy was ignoring him! Though in her defence, she was kinda distracted by all the hiking
Okay, so the ruins with the ice barrier must be the Cold Castle. And I'm guessing the Queen's Hive was found somewhere in that eastern swamp. Not that it really matters, since Plasma already took the Plate/Box from those spots.
Great Pyramid = under the desert, obviously. And the Sunken Shrine is underwater. No chance of us finding either of those without help.
The Grand Tree must obviously be in a forest somewhere, but I've no idea where - you'd think that a tree that big would be easy to find, but maybe it's underground somewhere? Or hidden amongst some equally big trees, possibly on another island like that one in the south-east.
Grand Castle, Mountain's Halls, and Dragon's Pride all sound like they'd be somewhere in the mountains. Dragon's Pride probably on top of the tallest one, and Mountain's Halls underground.
Fire (I'm not sure whether it's the Crucible or Forge, since both apply to Steel and Fire)
must be in Hamachi's volcano. Probably with the imprisoned Heatran nearby. That might even be what the Godslayer's are doing over there in the first place. Groundon already defended the Fire Orb/Plate from Team Magma, but the Godslayers will be much more prepared for him.
The Pit I'm probably having the most trouble with. It's likely at the bottom of a canyon or crevasse...but that could be basically anywhere. All we know is what Jack said; that it's not near to Murkoff. The rocky crags seem like a possible candidate?
The Grand Dojo I can see as either being disguised as a regular dojo, probably in the fighting city. Or it's on top of a mountain somwhere, and you need a ton of physical strength to get there. Cerebrum Tower could be literally anyway - in fact, I'm betting it's going to be somewhere obvious, and is using mind-magic to disguise itself/make people who see it forget it's existence.
And actually, speaking of hiding in plain sight....isn't that something the Normal temple would do? Hide itself by looking as unremarkable as possible? Because if I'm remembering right, you guys did find a castle when you first met Hoopa....albeit one that's now a pile of rubble.