The hardest, most time consuming portion of paint is the prep work. Just to paint say one wing, you have to mask up the entire plane. If you painted the entire plane at once, you would have less masking to do, depending on your paint scheme.
Also, painting all at once ensures that your paint matches in shade, texture, etc. No clear masking lines will be left between 2 seperate applications either.
This is comlicated further when using metallic paints.
I would just do it all at once, you can set up a cheap temporary paint booth that will work well with plastic sheeting, some cheap fans and furnace filters, and 2x2.