And ? Feeling relieved ? now you got it off your chest ?
I'm only an Arduino user, but I can answer a few.
The ATmega chips are microcontrollers: turn a led on, turn a led off, read a sensor. You know, just simple microcontroller things. Therefor digitalWrite() is a normal function. Do you have libraries with a lot of assembly code or tricks to make it faster ? Perhaps you use the Arduino for something that was not intended.
Things do change, and the Arduino changes. That is the way with our world. I bet you wear the same underwear for 20 years :o
Do you want Arduino to define the direction ? That is almost impossible. It depends on what users like and what kind of chips and hardware is developed.
Well, you know the default lame reply to all of this: It's open source, you can fork it and make it better 
However, you can also do like me: go with the flow and have fun 8)
Okay, the documentation is sometimes wrong and outdated. It is teethgrinding frustrating that I can not fix that. (Let's hope that AREF is no longer connected to 5V in the tutorial..... What ! 
).
There are line numbers, turn it on in the settings.
The prog_uchar did change, and you have to change the source code.
Most libraries support the ATmeg328P, and not every library supports the Leonardo. That's true.
Have a look at this new product : http://www.adafruit.com/products/2661
It's a Leonardo compatible board with Bluetooth included.
Adafruit maintains their libraries, therefor many Adafruit libraries should be compatible with the Leonardo.
Our "friends" at Arduino.org have a new development environment. And there are other IDEs made. I tried a few, but after all, I still use the normal Arduino IDE.