Wouldn't it be simpler to remove the SD card from the Arduino, put it in the PC, and then deal with the data there?
Not always. If I want to retrieve data from my rooftop unit, and the area is being pummeled by lightning, going to the roof of a 22 story building would not be a healthy thing to do.
I can see where FTP would be really helpful. I have not gotten that far along where I need that much data yet, but I can see it coming. Doesn't look that bad to me.
Don't let the thought that "nobody has done it before" is a reason for you not to do it. I took the time to write email sending code. I will post a link to that. It uses a two-way communication like you will need for the FTP protocol. It sends a command, then listens for, and serial.prints, the response.
http://arduino.cc/forum/index.php/topic,69647.15.html
Here is the formats for the commands and responses for FTP.
http://www.w3.org/Protocols/rfc959/8_PortNumber.html
I like the idea! 