Kira is obviously just the poster boy of Destiny since he's the most popular character. There really is no other reason, because as you guys say, Athrun is really the one being focused on all the time. Athrun was seen almost constantly in Seed too, making him the ultimate Seed lead. While I'm not a big fan of either of the 3 main chars, at least Athrun sort of develops a bit - thought it felt like he was back at square 1 during most of Destiny. (then again that applies to all characters... except maybe Yzak & Dearka).

Which also makes me think, why the fuck do people like a one-dimensional piece of shit moron like Kira?