I wanna know if I can change my 2005 Chevy Malibu's 2.2L engine with a 2005 chevy Malibu 3.6L and if It will be a easy swap or will I have to change the whole transmission as well ?

The efi is going to be the problem. Going from a I-4 to a v-6 will be some work. The tranny should bolt up though.

The quickest method would be to swap the computer and engine bay wiring harness. And all other mechanical parts that differ. Since it's the same model of car and the same year the rest of the car dash/gauges, tranny, fuel, emissions should work fine.

Method two is to get the PCM pin out from your I-4 car and the new motor. Compare and add the missing wires then reflash your PCM with the v-6 data. Can be a nightmare if you miss one thing. If the 3.6 your getting has a donor car I recommend swapping the harness and computer.