and could be used to code in a standard "Arduino" language (close to C)
There is no Arduino language! This is part of why some people hate Arduino, because they never took the time to actually understand what Arduino is and is not. If there really was an Arduino language that would be a good reason to hate it but instead we're using real, professional, programming languages. Sure, the IDE takes care of a bit of the less beginner friendly stuff but you can override any of that if you want.
The microcontrollers had to have the Arduino language loaded onto them, which in the case of buying an Arduino board, is the state in which they came.
Huh? Do you mean the bootloader? That has nothing to do with the "Arduino language" and is not unique to Arduino. In fact you can easily program an Arduino board or microcontroller without using the bootloader. Sketch > Upload Using Programmer
"It's easy"
I think this is the true underlying reason behind a lot of the Arduino hate. They learned this stuff the hard way so everyone else should too. It's threatening to them because microcontrollers are no longer the exclusive province of geeks. I actually think a lot of this technical stuff has been intentionally made more difficult than it needs to be for purposes of job security. If there is only a select group that understands the secret language then they can charge any wage they like.
"It's not perfect"
Very true but if all these geniuses spent 1% of the time improving Arduino that they did hating on it imagine how much better it would be. In the end, Arduino will never be for professionals, it was never meant to be for professionals. This doesn't mean professionals can't get involved with the project and use Arduino to share their knowledge. If you're some super smart kid on the fast track to MIT and a degree in embedded systems engineering then just skip right over Arduino, but for every one of those there are hundreds of people who are not willing to spend a week setting up a toolchain and reading datasheets just to get to that first blink when there are TV, video games, skateboarding, social media, etc. competing for their spare time. My theory is that if you can get them to the fun part fast then they will get hooked enough to go back and learn the basics. In the end Arduino might lead them to a career in electrical engineering even though they will not be using Arduino in that career, maybe it will be a new hobby, or maybe they'll just have a great learning experience and gain a better understanding of electricity, programming, and these amazing little chips that are in everything.