The Market Board will definitely be different as supply and demand is different coming from a mega server. That said it's both good and bad. When you need to buy things it usually costs more but when you want to sell things you don't have a thousand undercutters in a war to see who can drop the price below the actual cost of the item first.

As for dungeon queues and any instanced content, you would have the exact same queue on any of the Aether datacenter realms that you would on Gilgamesh. You also have the same cross server PF. Both of these pull from your entire datacenter, not just your server. So there are absolutely no downfalls in this regard as it's 100% the same queue.