Well, I got a chance to sit down and think about it, and I have come up with a plan for two sorts of hand controllers, both using the ST4 connector.
The first is a basic one which has just the NESW buttons and a speed select (low speed/high speed). This is essentially just four push buttons and a toggle switch. No power supply is needed, there are simply 5 lines that are ether grounded or floating.
The second is an advanced one which can control the full functionality of AstroEQ. This one is going to take some time to develop, but I am planning to make the code for interfacing with the AstroEQ as an Arduino class which will allow people to easily develop there own hand controllers with any functionality they desire. I'm aiming to support both the Mega and the Uno (and by extension Nano, etc.) with this.
Communication will be done using the Synta protocol in much the same way that EQMOD does (this avoids having to add tons of extra code to the AstroEQ firmware), though rather than being UART based, it will be SPI based with the handcontroller being a slave. The only reason for choosing SPI is because I screwed up years back when I chose the pin assignments - I used the second UART port of the ATMega162 as mode select pins for one of the motor drivers, oh how I regret that decision! But still, some careful coding and I can bit-bang SPI at 1MHz, so should work pretty well.
The basic one is in the current beta firmware and will be unchanged. The advanced one I have integrated the code into the AstroEQ firmware and have started work on the hand controller firmware, but I have no ETA on when that will be ready.