Looks nice. My concern would be hauling (my concern is always hauling, people complain about it constantly and then build fortresses the size of the Forbidden City). Is the entrance in the pit? I have two fortresses with entrances in the side of a pit and they work well. If so, then your depot is pretty far from the fortress given the two-wide hallways from the grotto to the fortress. Further, where would your killing field be? That long hallway from the pit to the grotto? Again, a lot of hauling if you ever wipe out a siege there. I've killed 80 in a large siege, each with at least 10 items dropped. That's 800 hauling trips right there. If I had that setup, I'd build a room off of that hallway with stockpiles for armor, weapons and goods dropped by attackers, and keep it locked so dwarves don't normally haul to them. Then when you need to clean up from a siege, lock up your other stockpiles and unlock those and once the bins are full, have them hauled into your fortress. If your depot is near, you might even just leave the narrow goods there and haul in the weapons/armor for melting or use.
My temptation would be to tighten up the fortress some so it's a little less sprawling and move it where the grotto is, and move the grotto south of the pit and east of the fortress. That may not work well on the map, however.
The only problem with rooms one level over the workshops is that the noise will reach the rooms and keep your dwarves awake. You need to keep about 16 tiles between your shops and rooms to prevent that, so putting them in one wing all 3 floors, with storage in the middle all 3 floors, and shops in the other wing all three floors would take care of that.
On the hauling issue, it is a concern... I'd planned on... Eventually, Carving out the bottomless pit into a spiral staircase so Caravans could come all the way to the bottom, and then maybe putting a Depot in the grotto... Defense is not an issue, The entrance to the, entrance, as it where is surrounded by a large 5zlelvel tall castle wall, and the entrance to that is lined with rather veil traps. If need be, I can slowly trap and mine the entrance leading down to the lower city itself.
As far as rooms go, I have to say I never knew a workshop BELOW a room would radiate noise, I always made sure to put rooms away from workshops.. Ill have to be more carful I guess here. Of course as the current layout is set up, there should be plenty of space for that,
