To be honest, I think if you're a programmer/developer looking at the Raspberry Pi as a gateway to basic electronics, you'd barking up the wrong tree and would be better off with one of the Arduino boards. With the Arduino you have plenty of resources, and the convenience of only needing the Arduino IDE and a USB cable to upload your program to the micro-controller. The Arduino platform can do a lot in terms of reading sensors and controlling circuits, and if that's all you want to do then a Raspberry Pi is far more than you actually need, and much more expensive than an Arduino too.
If you were a programmer, it seems like the RPi would be a better choice than the arduino -- you can code in the language of your choice instead of processing or C, and you can still control interface pins to the outside world.
Also, you'd probably do more with the Pi as a programmer beyond turning pins on/off -- for example, you could hook up a camera and run opencv, then write a small app to control a water gun that shoots squirrels off your bird feeding post.
When you start doing more with arduino, you typically want network connectivity, and most of the wifi/ethernet shields for the arduino are the cost of the entire RPi computer. I think the RPi does fill a good niche in the hardware world.
If you want to be network accessible, the Raspberry Pi costs about the same as an Arduino with an ethernet added.
As far as programming, simple is easy on Arduino. The limits are further away with a Raspberry Pi. Say you want to log some data for later analysis. Trivial on a Pi. Anything more than a few kilobytes and you are wiring an SD card to your Arduino.
I'm currently using Arduinos for well defined, simple functions, but for more complicated functions. I will use Raspberry Pis where the BeagleBone CPU is overkill, but Arduino will always win for low power use.
Arduino's are usually $30, though you can get the clones for $20. The ethernet shield alone is $45. The cheapest Arduino-a-like with built-in ethernet, as far as I've found, is the Nanode v5, at $40 in unassembled kit form.
Many of your other points are valid. For tons of projects a Pi would be overly complicated overkill, but I can think of many times when I'd want more video in/out capabilities, plus the ability to blink some lights, drive some motors, and accept non-usb sensory input.
Just get a teensy[1] board, and hook it up to the Rasperry Pi.
I'd like to know what kind of stuff you can do with the GPIO pins directly on the Pi, via /sys/class/gpio. Are they just digital (0,1) or they can read voltage levels too? (electronics newbie here)
I really like the idea of the controller being a familiar environment with a high level programming language. I'm sure that Arduino can do all the same stuff, but it seems like the learning curve is far steeper.