This question is taken from Ultraman Lah! I hesitate to post there my answer, which incidentally is almost the same as the first posted reply, because it may seem like I copy his answer. So I'll just spam my own journal.
Sakocchi is my most favorite. :) To me, he's the coolest captain ever. He is capable of relating to all of his subordinates (even to someone not human like Mirai) and often gives them good advices.
Following closely after Sako, it's a tie between Tiga's Iruma and Nexus' Wakura. Iruma is just so good at understanding her subordinates. Wakura is also very understanding, particularly of Komon and Nagi.
Wakura's actor, Tamotsu Ishibashi, incidentally also appeared in Tiga; his character has a little disagreement/rivalry with Iruma in ep 38.* Irrelevantly, I thought both he and Iruma's actress were great in that Tiga episode.
*One of sennetari's fascinating(?) facts. She isn't claiming to be the only person who knows it, but probably the only person who would often mention such a trivial thing.