I know you can communication with your arduino and matlab through usb but could it be done wirelessly and still work properly?
The bits being streamed back and forth don't care if there is a wire carrying them, or not.
any other problems you think I may run into?
Tons of them. The key is to anticipate as many as possible, and to deal with all of them. Do not wait until the last minute for any part of the project. If you have a problem, either deal with it now, or revise the scope of your project.
Just getting a quadcopter flying straight and level, and be able to control it from the ground is a big project. Making it actually perform some useful task is over the top.