Sure, but with Arduino you're still floating on top of the Wiring libraries for almost anything you do. Coding a bare-metal AVR is a bit different:

http://florin.myip.org/blog/how-make-halloween-creepy-blinki...

There's no significant difference, unless you want fully predictable real-time behavior (of which my piece of code is NOT an example, but that's all I have online).

Most people shouldn't care.

You can start with a straight-up Arduino program and mix in as much bare-metal AVR code as you like. There's nothing in between you and the hardware, and that's important when you discover that time matters.

I've done a fair amount of embedded work, some with AVRs and some with various ARM chips, mostly Cortex-M3... I always start with the nice libraries because why waste your time reinventing that stuff if you don't have to? But when you have to reach deeper and gain finer-grained control over your hardware - and almost every project eventually has to do that eventually - it's really, really nice not to have some VM in the way, not to have to start over in a lower-level environment.

Thanks for sharing. I'm working (very slowly at the moment) on an AVR simulator in order to teach myself C. I think this is a great little program to compile and test with.

The Arduino library provides a lot more flexibility compared to the bare AVR + libc, but at the expense of performance. Notably using digitalWrite() can be up to 50x slower than writing to the port registers directly.

Yes, but you can still write to the port registers directly. Using the Arduino libraries doesn't lock you out of anything. There's a smooth, continuous path from high-level C++ abstractions built on the Arduino primitives down to the bit-twiddling low-level C world.

If you're walled off in a Javascript VM, you can never have that kind of transparent access to the hardware - which seems like a big problem when you are building electronics, and controlling the hardware is the entire point of the job.