I'm currently working on my second PCB iteration of a design and am trying to cut out everything that is long term unnecessary from my board. Right not I am able to upload to an atmega2560 using a USBtiny and also a AVR Dragon using both AVRDUDE and Atmel Studio. Once I have uploaded the sketch/firmware to the atmega2560 I am simply sending it i2c commands from a remote master to run certain functions. What I am wondering is if I remove the the 16u2 from my designa and simply use the atmega2560. should the device function properly without the USB-to-Serial converter. I can't see any reason why it wouldn't, but i'm fairly green so I', not confident in my assumption. Thanks for the help.
Unless you're using the USB-serial converter in your sketch, or to upload your sketch, you can remove the serial adapter no problem.
If you are programming it via an ISP programmer, you have overwritten the bootloader, and couldn't even upload over serial if you wanted to (without bootloading it first) anyway.
Yes, the USB/Serial adapter can be reduced to a header you can connect an FTDI Basic or equivalent to for debugging via Serial monitor. I did the same here on this 2560Mini board. Processor on top, crystal and some Rs & Cs on the bottom.
ICSP header for bootloading/fuse setting, FTDI for serial interface/debug. http://www.crossroadsfencing.com/BobuinoRev17/
