Indeed, but the version packet is probably the smallest packet of all the ones sent, so we’ll gain more elsewhere. Also, keep an eye on the main point. The fact that protocol buffers are smaller is a nice aside to the fact that they’re Forwards compatible and make bitcoin portable between languages.
Debugging is also easier with non-custom formats. Instead of being the only one using it, you have many other people on different projects looking for and fixing bugs. You also often get tools for decoding/displaying the packet to make it easier to see if something is wrong. IMHO the size of the packet is the least important reason.