I've explored all of Fort Joy. It's got a shabby Ghetto for the prisoners, it's got a prisoner kitchen for the prisoners. It's got jail cells for troublesome prisoners, it's got a Kangaroo courtroom to sentence prisoners to cartoonishly evil punishments. It's got luxurious quarters for the upper Magisters, it's got a gigantic, cartoonishly evil torture room. It's got a dock and workshops at the dock.
Do you know what's missing?
Barracks for those generic soldiers. A kitchen and mess hall for those generic soldiers. A supply and food storage room for the soldiers. An armory for where they keep their generic weapons.
That's all missing, and it shouldn't be.
This can even tie into improving the economy of the first island.
What do the prisoners (and the Seekers) need? Food, water, medicine, alcohol, narcotics, clothing, weapons, armor, and small valuable items for bartering. Those are the things which matter to them. Maybe even books, and decks of cards for entertainment or distraction.
What do the prisoners NOT need? 8-foot tall 200 pound paintings of Alexandr. So why are they so valuable? Those should sell for pretty much nothing because no prisoner or Seeker needs a painting. A juicy pear swiped from the guards quarters should be worth a lot. Cyseal was under siege, but inside the town life was fairly normal. Fort Joy is not the usual town and should not follow the same economy rules as Cyseal.
The first island should have its own set of items identical to items found later in the game, but on the first island, they sell for different prices. Or better yet, they're the same items, but there's code to alter the prices after you leave, so that 15 gold pear you filched becomes only worth 3 gold on the next town after escaping the island.
So, how does different items tie into the need for an additional floor? It's simple. That upper floor could have supplies which are valuable in the prison economy. Instead of a couple paintings worth hundreds of gold, you could find high-quality rations intended for guards which sell for 30 gold each or something.
You could even add in quests from prisoners to get medicine/medical supplies and decent food. There's quite some potential for what could be done here.