I think arduino has done wonders for getting people started, but it would be great if there was a similar ecosystem for people who are further along than blinking LEDs and building something of significance.
The thing about embedded is that you're crafting a very specific hardware and firmware design for the task at hand. The project may begin with a generic setup like Arduino or Beagle or Rpi, but at the end it's a totally unique animal. There's no way any graphic or assisted design environment is going to be able to handle it all.
Hell, FPGAs are Jedi-Master class devices as far as I see it. This is the kind of firepower you call in when you have something that no off-the-shelf micro can do, like emulate an obsolete processor, or put 128 of them on one chip, or hash Bitcoins, image processing, etc etc etc.
For example, it would be cool if there was some sort of software that would let you design multiple-chip setups that would usually require breadboarding, but then run the whole circuit on the FPGA. That design could be transformed straight into a PCB that's ready for fab with the discrete components.
I actually see a lot of potential in devices like the aforementioned Cypress PSoC. If you're not familiar, the PSoC family involves chips that have a core microcontroller with ram and Flash but also have a number of analog blocks inside as well. ADCs, capsense, op-amps, logic gates, muxes, comparators, timers, etc. You can use the Cypress IDE to wire the components up and connect them to I/O pins. The IDE can generate your configuration, or you can optionally reconfigure the chip while running via internal registers.
So it's kind of like an FPGA-type solution as you suggested. When you start developing with these chips, you're really creating hardware from software. It's interesting stuff.