Shigure has always wanted to taken a more active role with training Kenichi, like someone said earlier. It's just that, Kenichi is afraid of weapons. However, I think are implications that Shigure has more than masterly feelings for Kenichi. Although all Kenichi's Masters seem to have a certain soft spot for Kenichi, her softness towards Kenichi surprised Kenichi. Like someone said earlier, she probably isn't aware of this either.
On her reliaibility, Kenichi views most of the Masters as "unreliable", or at the very least, reckless. He views all masters this way, except Akisame (who he views as harsh and efficient) and Ma (who is actually unreliable (very unreliabily, really) in the general sense but not reckless).
On Miu, it's quite obvious she has, at the very least, sisterly feelings for Kenichi, but probably more than that. Her women's intuition meant that she thought it was possible that Shigure liked Kenichi
On Alignment, I would say Kenichi is definitely Good, but I would place her Neutral Good leaning towards Lawful Good. I would say Akisame is Neutral Good leaning Lawful Good as well. Both Ma Kensei and Miu are Neutral Good, while Sakaki and Apa are Chaotic Good. I have a hard time placing Shigure, but I would guess she's a Neutral leaning Good and leaning towards Neutral/Chaotic. I have no idea where to place the Elder... he's all over the place.
As for Yami, I would agree that they are much less cohesive group. I'm getting the feeling that "Killing Fist" is the only thing keeping them together, and even just barely then. They seem have different goals, methods, behaviors, and beliefs (despite being Killing Fist). They also have poor unity and communication. I suspect that some of the Masters of Yami wouldn't be completely heartbroken if the organization of Yami as a whole fails. As for specific alignments, I would say that Diego Carlos is probably Chaotic Neutral, and Alexander Gaidar is probably Chaotic Evil, leaning towards Chaotic and less towards evil (though this very much).