On the subject of what the name will be, it really depends on what exactly we are looking for. Are we going for individual code names, or are we going for something more along the lines of a squad name? Also note that we are supposed to be secret weapons. So the name should not be too revealing, or revealing at all, as to the nature of what we are. Along with that, the name would probably not even be mentioned much, espically in the presence of civllians, as the military would probably want to keep us as much of a secret as possible. So, all in all, it would probably only be a name that would only be said by the generals, and ourselves when reporting in on radio or something, assuming we will be using that sort of equipment.
So if we are going for individual codenames, simply the names of the Pokemon that we were merged with could suffice, plus it would be sort of symbolic, as if we were accepted as citizens of that planet or something. Although considering how it was introduced that we have the consiousness of the Pokemon inside of us apparantly, so that might not work out very well. I have no suggestions if we are looking for a sqaud name.