The early prototype had USB ports, an Ethernet port, and a serial port. These connectors weren't intended for the final product but it made working on the prototype easier.
The early prototype is also quite large—about 5"×7" and roughly two inches thick. "Seems large now," our source said, "but at the time it was really impressive seeing basically a version of OS X running on it. "From the looks of the logic board photos, Apple had a decent idea in 2005 of where the iPhone would end up, even if the final product became much more integrated.
Notably, the prototype used an ARM9 chip revealing that Apple intended to use Samsung made ARM chips from the beginning. The chip shown below was reportedly clocked at 200-233MHz. The first iPhone was released in 2007 with an 620MHz ARM11 chip underclocked to 412Mhz.
Take a look at the photos below...