I get the feeling that plot consistency wasn't really their primary concern. But yeah, one of the things I found most frustrating is that a lot of these issues seem terribly obvious and could have been dealt with by a couple of lines of dialogue, and it seems so lazy not to deal with them.

I like Kirk being smart, but truthfully, the whole rebellious leader thing irritates me. Purely a personal objection--I realize lots of people love that--but it's not my thing. Which is probably why Spock was my favourite character when I watched TOS as a kid.