I think choosing the best microcontroller for the project in also about what you want to learn. If you want to learn about microcontrollers, you should probably use something else than arduino. But if you don't know much about electronics, and just want to build a working device, I think arduino is a good choice. Also for first projects, using Arduino gives you a soft start.
I have used both PIC and Atmel. I have often found Atmel datasheets easier to understand and also they don't seem to have quite as many serious bugs. Often PIC controllers have been cheaper though. I think you can pick either of them or try both, there's not a lot of difference in non-critical applications. Some people say that Atmel is shit or that PIC is shit, but they're just a bunch of old stubborn people (I think your lecturer falls into this category too). If you have a critical application (need fast ADC or clockspeed etc), then you will probably find that one might be better than the other in the specific application.
If your lecturer says that everybody uses PIC and that's why you should too, he is not leaving much room for innovation. If everybody thought like that, nobody would come up with anything new. I just hate that mentality. If I were you, I would choose an Atmel product, was it Arduino or something else, just because I was told not to.
Btw, greetings from Penang
do you need to design a new PCB for the application at this point? If you are working on a prototype it could be simpler to use a development board such as Microchip's microstick or Explorer 16 and when you have a working system then take it to a PCB.
