Most everything you want is already out there, but it's going to require some work on your part. All the popular front ends out there are attempts at being all things for all people. Of course, they can't, so everyone will find certain things they like in one and not the other. So, you have to invest some time and learn how to dig in and configure it for your needs. For example, you want to graphically drag and drop your layout? Not sure about the others, but AtomicFE has that - click on an element you want to enable, and drag it to the location you want. This cannot be done via the front end, you will have to run the layout editor program. While none of the front ends out there (besides Mame32) have a folder structure, you can mimic the same thing by building custom game lists, something all the front ends can do. But again, you will have to invest some time and build these lists.
A virtual keyboard would be very useful for certain functions if the cabinet has a trackball but no keyboard.
AtomicFE offers a virtual keyboard to enable searching for a game. You press an assignable button to bring up the keyboard, and use the joystick to select the keys. Everything else would require a keyboard to configure the actual options of the front end however...
The main thing is that you design your layout, options, etc, and then build it. Once it's done, then fire up the front end and play. Once the thing is setup, do you really need options like dragging and dropping the layout, etc? If you do want to make changes, updates - is it really that important to be able to do it within the front end? Why? When you can just fire up a configuration program, make the changes, and save? AtomicFE offers a real-time preview of the layout if you really need to see what something looks like right away. And I believe Mala and GameEx offer something similar.
I think between AtomicFE, Mala, Mamewah and GameEx you're pretty well covered - one of these four has got to be able to do everything that you need with a little creative thinking/configuration.
Perhaps you find so many options in the front ends intimidating? Try AtomicFE's plug and play modules, or GameEx's automatic configuration - they may be more to your liking.
What it really boils down to is that you will have to do some work and figure out how to configure one of these front ends to make it into something that you are happy with. Out of the box, almost all of them aren't what anyone is looking for. However, they all have a ton of options to make pretty much whatever you want. There's a lot of great people here that will take the time and help you if you have questions on a particular front end, plus additional forums for each of the popular front ends out there. Now get to work, so you can play!
