I've been working with arduinos for quite some time now and finished some cool projects. The problem I have with arduino boards is that programming them is extremely simple and I have virtually no idea what is happening on the inside (you don't learn much about microelectronics while using them). I am pretty fluent in C and C++, however the arduino's version of these languages is very basic. I was wondering what microcontrollers/microprocessors are being used in the industry and how to implement them in my projects? I've heard about AVR, ARM, ATMEGA (on it's own), etc. Are those the ones that are being integrated in professional (commercial) projects? I've seen the MIT's video about autonomous robotic plane - https://www.youtube.com/watch?v=kYs215TgI7c, where they have used an "Intel Atom Processor". How can you use an Intel Processor to control electronics? Obviously an Intel processor is overkill for my electronics projects, however I am still curious how it can be used.
If you're looking for something easy to graduate to from the arduinos, consider using an arduino without their IDE. It's then pretty much the same as any other ATmega dev board. If you go to the Atmel website (now part of the microchip one) you can download Atmel Studio for free. This is a fully featured IDE based on Visual Studio. You can get a plugin for it which let it work with arduino files... but if you want to move towards more professional use, avoid it, and write complete C (or C++) files. For the ATmegas, with their very limited RAM, I'd stick with functional rather than object oriented programming. I'd also avoid the using the heap/malloc/free unless it's really necessary.
From there, you can look at development boards, aka dev boards. That's the technical name for a microcontroller with the necessary supporting hardware on a PCB so you can try it out. They are available for many microcontrollers, though often only one per family of similar parts. They are more expensive than arduinos, partly because they are not made in such large numbers. Unlike Ardiuinos, they are also usually laid out by the manufacturer exactly how they intend with the chip, so they can be a good place to look for hints when laying out your own first PCB.
Yes, the Arduinos somewhat hide the complexity "under the hood". But working with professional microcontrollers and tools is not very different comparing to working with Arduinos. The Arduino ecosystem has just built kind of a standard across slightly different MCU types.
If you want to know which MCU's are used in the industry, why don't you look directly at the different Arduino boards? E.g. the Arduino Uno R3 has an Atmega328P MCU, a very simple 8bit type from Atmel (now Microchip).
The PRO tools give you some really nice features that are not provided in the Arduino ecosystem, like e.g. single step code debugging, code and power profiling, virtual ports and a lot more.