I checked the datasheets and the overview pages on Atmel's site for these ARM cores, and I think they are amazing. Especially looking at the ATSAMA5D41, this would go well with a project I am working on. The only problem is, is I have no idea how the "pins" work. I cannot distinguish any individual pins function i.e. USB, SPI, UART, TFT Display Control, etc. Can someone please explain the pins or at least how to read the pin assignment datasheet because I am so lost.
Looking at the datasheet, refer to page 10.
The left columns explain the general functionality of the ball - I/O, power, ground, etc. The middle columns (PIO Peripheral A/B/C) explain which peripheral functions can be mapped to particular balls. The right column explains the boot configuration of the ball - so, for example, the external memory bus balls default to being a memory bus so when it boots up it actually runs.
I should point out a couple of things that may impact on your love for this processor.
Firstly, it's offered exclusively in a BGA - ball grid array - package. These really require machine soldering, and higher pin count fine pitch BGA packages can be quite challenging to lay out (or at least, to lay out well).
Secondly, this is a microprocessor (MPU), not a microcontroller (MCU). It's not clear from your question whether you realise this; you may actually want an MPU. If you're looking for an MCU though, then this is NOT your baby.
An MCU is (generally, although not exclusively) a single-chip solution for smaller embedded designs. They might have 1kB to 2MB of Flash, and anything up to perhaps 256kB of RAM. They might run an operating system, but it will most likely be an RTOS, not a full-blown PC OS.
An MPU is the core of a full-blown computer. They generally require external memory, both volatile and non-volatile. They typically have clock speeds in the 100's of megahertz. They are designed for running a PC-style OS, like Linux; think Raspberry Pi or Beaglebone. Designing a circuit board for an MPU is very non-trivial.