1) Chief's Halo 4 armor is artistic interpretation of his Halo 3 armor.

2) They didn't consider to give the CGI Halo 2's armor the Halo 4 armor, because they either knew that fans would throw a massive temper tantrum over such a change, or because they just didn't consider making such a change.

3) They'll continue to use nanobots as a cover-up for an unseen problem that some of the core Halo fans have.

4) We're just going to have to 'deal with it,' which I'm actually okay with. I understand if it's an artistic interpretation. If that's not the real excuse, then I think it should be (personally). Fans aren't okay with "nanobots," and I don't see what other explanation you can provide. So just say artistic interpretation, and leave the issue.

343 just took over an entire franchise with the Halo IP, with a new team, so mistakes were going to happen. They managed to produce a game that is up to par with the other Halo titles (IMHO); I feel that they've done an amazing job overall.