1) Arduino IDE and Arduino Uno (or other boards) are good for beginners because you can quickly get familiar with AVR chips, you can blink your first LED in 30-60 minutes from the moment when you get the Arduino Uno board. Apart from that, there is no other serious advantage.
2) Arduino IDE is quite inflexible. It is designed to work well with the Arduino boards it has in its list. If you want to use Arduino IDE for stand alone AVRs you run quickly into huge complications and the entire programming process starts to look more like hacking than serious work.
3) Another problem with Arduino IDE is that it does not have a debugger, it does not have a simulator. You can not run your programs step by step to find errors.
4) The hex file size generated by Arduino IDE is also a problem. A source code that just blink a LED, once compiled, generates a hex file greater than 1 Kbyte. Same code in Bascom is below 250 bytes and in IAR below 100 bytes.