The cartridges plug into the bottom of the unit, much like the GBA SP does. The cartridge port is slightly off-set to the left side of the unit, making room for the headphone port on the right. That's another big deal: instead of the proprietary headphone port of the GBA SP, the Game Boy Micro uses standard 1/8" headphones. On the top of the unit between the L and R buttons, the system has an EXT port that will be used for charging the internal battery as well as provide a plug-in for the link cable dongle that will be made for the unit.
The EXT port is proprietary to the Game Boy Micro, looking similar to plug-in ports for a cellphone.