As a newbie I am digging through the available documentation and I have seen, that you are using linear regulators on your current EZ-B design to step down the battery voltage of ~7.5V to 5V. This is very energy inefficient for higher currents (e.g. 3A), because you are throwing away (7.5-5)*3A = 7.5W... As a result you need large heatsinks for your voltage regulator and your battery will be discharged very soon.

A better approach would be to use switched DC/DC regulators. They have a much higher efficiency (>90%) compared to linear regulators. As a drawback the voltage output has an increased ripple, but this can be easily compensated with some capacitors. And most digital devices don't care about a ripple of some xx mV and you get rid of the heatsinks.

To make life easier, there are already some complete DC/DC modules in a hobby friendly SIP package available. As an example:

TI PTR08060, 4.5V-14V, 6A or TI PTR08100W, 4.5V-14V, 10A

The minimum input voltage of these modules are ~6V for a 5V output, but I guess due to the high efficiency this is ok for most users. Maybe you can provide a second voltage connector, directly connected to the 5V for the micro and the 5V for the I/O voltage, if you want to provide a direct (or different) 5V power source.

Just an idea to improve the already fantastic EZ-B... :D