The Superflat customization screen has been left unfinished for a long time. It would be nice if they added an interface for easy customization. Here's my ideas.
First, there should be a block layer screen. There would be two lists, one on the left, and right. The left list would list all the blocks. Variations of blocks with the same ID will be included, unless they are technical blocks. The list on the right would be what blocks are going to generate in the world. You can scroll through the left list of blocks, and click-and-drag them over to the right. You can also click and drag blocks between layers, so you don't have to start over if you forget something. When you move blocks to the right, there would be a number beside them, which shows how many of that block wll generate in a layer. Of course, you can change it to your liking.
There would be another screen that has biome/generation options. You can choose which structures you want to generate in your world, such as villages, strongholds, and others. It would be a drop-down list, with about every structure listed. Each one would have an empty box, which you can check if you want the structure to generate. Then, there should be a biome options list. It would work the same as the previous one, but you cannot uncheck anything if there's only one biome checked. This prevents the user trying to make 'no' biomes generate. At the top of the list would be an 'all biomes' option, which does what it says.
Lastly, there would be a miscellaneous options list, which allows you to toggle caves, decorations, water/lava lakes, etc.
That's it for my suggestions, please tell me what you think.
One thing to note - you can't just select which structures to generate because they also have parameters to change their size/distance/frequency, which is extremely important for a truly customizable world (the most annoying thing by far about the so-called "customized" world type is that they only let you turn structures, caves, etc on/off with absolutely NO options to make them bigger/smaller and more/less common without modding the game). See here for details (ironically, some things, like lakes, can only be turned on/off in Superflat but can be customized in "customized" - why not allow both world types to be able to customize the generation of every feature? Really no excuse except for sheer laziness as they both generate the same way in both world types).
It wouldn't hurt to add in a screen that lists every type of structure and sliders for each one (2-3 in some cases; for example for caves you have a variable that changes the size of cave systems and another that determines how often they generate; villages have size and distance; mineshafts chance; strongholds distance, count, and spread, and so on).
Also, Superflat is only capable of using a single biome (they use the same chunk provider as the Nether and End, both with only a single biome to use) and it wouldn't really make much sense to add in multiple biomes to a world type where terrain is generated in fixed layers (e.g. deserts wouldn't have sand unless specified in the options, oceans no water, etc). Actually, I believe you can make something similar to a multi-biome Superflat world by messing with the settings in customized.
Personally, I think the customized world type needs to be expanded upon first since it enables much more variety in what you can do.