>First off, remember that I'm talking about the cheap chips, <$30 or so.
No we don't. Developer boards are also used for high-end stuff like industrial controllers.
>I don't want a bunch of options for storage controllers on the board. Instead I want the pins available to wire to the storage controller of my choice.
Not going to fly. You need to either have some kind of universal bus (like PCI or PCIe) for data transfer which is not usually acceptable or have several versions of SoC with different integrated controllers (and that's what usually happens). Oh, and you'll also want different version with different amount of built-in storage.
>The more complex you make the board, the more 'extras' you put on it, the less flexible it is and the more likely it is that someone will want something else (and the more expensive it will be)
Developer boards are just that - they are used for DEVELOPMENT. They are not intended to be used as general-purpose computers, but instead they are intended to mimic the target system as close as possible but no closer.