A number of reasons;
- integral FPU
- largest SRAM & flash of all the ARM MCUs
- highest number of timers
The Cortex M4 parts are pretty beefy, and price not much greater than Cortex M3, so I see the attraction.
I've just taken a look in the ASF documentation - whilst the SAM4E-EK board is not supported, the SAM4E devices themselves are, and the typical features present on the eval boards such as LCD displays, QTouch etc are not features i'm remotely interested in using. The target application for my personal dev board is automated control applications, without the need for screens etc.
Ah, my mistake, I was looking at older version of ASF. The latest ASF has SAM4E stuff in. One thing Atmel are pretty good on, is documentation, examples, reference designs, framework code, etc, and they make it all easy to get hold of. So if I was starting with a new design, Atmel is a good choice from that point of view. I actually prefer NXP or ST ARM chips over Atmel, but Atmel ARM chips are good enough.
Perhaps as you mention - working with the SAM3X in my own board first would be a better option, as a revision down the road to switch to the SAM4E would be less of a jump, but then again - my board design currently uses a AVR 2560, so that board revision from AVR to SAM3X would be enormous as is, so it seems to make logical sense to jump straight to the intended device.
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.
If you can find the right eval board, extra cost incurred may be only a few $. Official manufacturer eval kits tend to be stupidly expensive, with a few notable exceptions (e.g ST Discovery boards) but there are people like Olimex who create low cost options. If you need to run a sample project built for IAR, Keil etc, there are usually free/limited "lite" versions you can use, but for Atmel you probably don't need to look further than Atmel Studio.
This switch isn't planned for probably 9 months, I'm just looking to get thoughts into it - but ultimately how to upload to the SAM devices from Atmel Studio, like I say - I've only ever worked 8-bit with the AVR ISP MkII programmer. (or of course the Arduino IDE)
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.
Maybe what I said sounded a little too negative, Cortex parts are relatively easy to use, though still a step up from AVR. There has never been a better set of freely available tools and resources to help designers. 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.