The free toolchains, IDEs, user support, reference designs etc are what are keeping me so attracted to Atmel. The Freescale Power PC MCUs are undoubtedly some of the most capable out there, but the IDE is a paid product - and everything seems very hush hush compared with Atmel products.
Maybe what I said sounded a little too negative
Not at all, I understand entirely! I appreciate it's a little more than a small mound to climb.
I wouldn't necessarily recommend SAM3X as first option, I was thinking more of something like SAM3S. I am a believer in incremental change, or at least starting with something that is known to work. I would generally start with an off the shelf eval board, and find an IDE with a project ready for the board (setting up all the project options is tricky enough). Then I go to my own hardware, a different toolchain, and create projects from scratch.
I initially said the SAM3X as it is of course the chip that comes on the Arduino Due board, but really - the more I've thought about this, the less I see the point in using the Arduino IDE and learning to use a more powerful environment such as Atmel Studio.
I see what you're saying, but really - the eval boards don't appear very attractive to me, partly due to price, but predominantly as mentioned due to the fact they mainly feature the sort of things I'm not using.
Atmel Studio + Segger Jlink EDU version is a great combo for bare metal programming. The ASF provides a pretty useful peripheral library, but not as easy to use as Arduino libraries.
This response, and really the question that prompted it is where I'm lacking on the knowledge front mostly. Just taken a look at the Jlink unit (
http://www.segger.com/j-link-edu.html), so - are devices like that programmers, or just debuggers for the JTAG interface? (JTAG is something I've never worked with before either)
If yes, do they program over an SPI interface the same as the AVR ISP does with the 8bit AVRs?
So go for it, just beware there may be a fairly steep learning curve. Some people enjoy the challenge, and if motivated it's not a problem.
I wouldn't be here if I wasn't

Thanks for your input so far! Greatly appreciated.
EDIT -
The Cortex M4 parts are pretty beefy, and price not much greater than Cortex M3, so I see the attraction.
Saying that, I can't seem to find the 4E chips for sale by any of the big vendors in the UK. Or anywhere outside of the UK for that matter...