Storage, can't have enough. Even if you just put a set of racks with a bunch of containers on them in a small room, storage and lots of it. Look at the Mini Armory mod for an idea of an efficient storage system that does not take up a bunch of space. Have a container or two near the crafting stations so that all one has to do is swivel to go from container to station. I frequently just grab everything in the container no matter what I am going to make, as sometimes I putter making new things.
If you put it underground, then you can provide a tool that lets people put the entrance anywhere. Otherwise, the exterior does not matter much to me unless it is one of those compound type homes. Just give me a way to get in, and I am good to go. Take over a stock house in a town even, if fits your design ideas, or better, add an exterior basemant door to a home somewhere, that way your not changing an original cell. There are some basemant doors already in the game resources. If you do take over a building, check with the Nevada Interiors mod and others that add things to existing buildings, so there is no conflict.
Nice atmosphere, does not have to be elaborate or showy, but gives me a reason to come home. And, it looks like I care, at least somewhat, about where I live.