Kira being an "Ultimate Coordinator" is a reference to his birth and not to any abilities he may have. The creation of a First Generation Coordinator like Kira is a process similar to in vitro fertilization with the genetic manipulations taking place during the earliest stages of embryonic development, after which the embryo is reinserted into its mother for gestation. During the period of genetic modification the child's parents are allowed to select any characteristic that they would like their child to have such as their hair and eye color maybe even their gender. However there is a discrepancy between how a Coordinator fetus is intended to develop and how the child really turns out. In many cases unwanted genetic traits would appear in the baby, arguably due to the inability of the mother's womb to pose as an adequate environment to support the genetic modifications. Ulen Hibiki, proposed the usage of an artificial womb to circumvent the natural womb's shortcomings, meaning that the Coordinator born will only possess what the parent's deem as desirable traits.
Kira was the only child who was successfully born from the artificial womb without any "undesirable" traits and was thus labeled by the scientists working on the project as the Ultimate Coordinator.