When it comes down to comic book fashion design, there are two basic camps, depending on how you perceive the world. Ignoring super-heroes and cyborgs for a moment, the issue is more than just aesthetic, even though your illustrator may disagree; there are issues of how gritty you want your comic to look, and dear you want human life to be. Those looking for a gritty story where human life is cheap usually ignore body armor in favor of decent fashion. Not only does it underscore that human life is cheap, but that it's more important to go out looking good than actually being good.
It also makes for an important point regarding relationships: People are going to have relationships that tend to the superficial, and that are more important for the political relationships they represent than the actual relationship. Some are going to be based solely on how pretty or handsome the characters are, and will likely last only as long either is in fashion. It also means that ugly characters are going to be easily aggravated, as the only relationships they have are those that they pay for or force. The world may be pretty, but the people are ugly.
On the other hand, if you want to show that human life is important and worth clinging on to, then put everyone in armor. The armor doesn't just act as a protection against bullets and blades; it also shows the necessary armor that people put on in order to protect them life. People are likely to not expose themselves very often, and when they do they are likely to go full bore. Relationships are going to seem forced and usually long term; once someone finds he feels comfortable with he is likely to do whatever it takes to keep that relationship. Even those that appear open are likely to keep some part of themselves hidden. This world will be filled with a lot of icebergs, where everything is chilly and there is a lot more going on then what appears.
Of course, you can mix the two approaches as desired, either on a person-by-person basis or creating a split world between those the pretty and the armored. That could make for some very interesting characters, especially as their personalities would have a very visual aspect to them. Ultimately, when you decide where you are on the armor debate, talk it over with your illustrator and see what the two of you decide. Regardless of that decision, it is one worth debating.