It usually boils down to whether you're a camper or not. I have the large Valley Oval hatch on my rear deck on 3 boats and would never do that again. 2 - 8" circles would have done me fine. On another boat I have a 6" and 8" circle and its perfect. I don't camp.
Also do you have a drop down skeg. Or if you decide to put one in sometime, its nice to have storage closer to the back bulkhead and the skeg box a little past the rear hatch opening. I would move your back opening more towards the cockpit. If you have a paddle shop near you with real kayaks, you can always check them out for an actual visual feel for what looks right for you.
I usually have a dry bag with some extra clothes, some extra water and often a lunch in another small dry bag. Then a utility bag with some first aid stuff and duct tape. Between two compartments its not much at all that I carry.
I understand that you may not know what adventures the kayak will bring you. You can always cut a larger opening too and just make a lid. To make the lid stiffer, you can fill the weave on the underside. But you'll be surprised how stiff it will be when you cut it out.