The advantage outside the IDE is smaller code and easier to make your own library's
The disadvantage is you have to write code for just about everything which is built in.
What differences and problems of programming Arduino and other devices?
The main difference is that, compared the other computers, the Arduino is very small. It has very little memory, either for programs or data. It also runs very slowly compared to other computers. But, with the Arduino, you have access to hardware I/O pins that you do not get on larger computers.