I'll try my best to explain them (spoilers):
1) "But the whole airplane hook business?"
The hook thing doesn't make sense if it was 'random airplane', but Alfred mentioned someone would 'do it for cash' before the trip, so this plane was in on it, they were flying around and saw the parachute and swooped in to pick them up. I'm sure there are pilots (Wash, hehe), that could do this.

2) "Lucius Fox giving away Batman's identity."
I think the key here is that a client would have to 'fund' the research, so as an accountant (not lawyer IMHO), you would expect to see A) payments for the research or at least B) a contract laying out payment for completion of said research. The only person who could divert funds of that scale (not really slush money) would be the CEO.

3) Rachel Dawes actress change...
Suspension of disbelief, different films, this happens from time to time, heck the actor that portrayed batman in the last series (keaton, clooney, kilmer), changed, why such a stink about someone not as central to the story. Plus, I think it was MUCH improved over the Holmes rendition.

4)Fight scenes
Can't really agree with this outing, but the fight scenes in the first one definately was distracting. Personally I like the chaotic feel and greater use of the gadgets/environment in this one... batman is a great deal about the gadgets. I can see "punch, punch, duck" anyday; using a grapple to trip up hostages so that they don't get shot mistakenly is, IMHO, more of what differentiates Batman from Joe Kung-Fu.

5)"The ending makes no sense"
Lots of sub items here..... but the Dent as a Hero has to do with the fact that people can't identify with a man wearing full body armor fashioned after a bat, using technology that even the government hasn't been able to create (I know I can't, perhaps you're a billionaire vigilante yourself). Dent, on the other hand, is a person who could be any one of us, and people would like to think they could be, standing by their principles in the face of adversity for the good of all man, risking their life even, so that the bad guys (i.e. identifyable humans doing bad as opposed to villains we can't identify with doing evil... again you could be a clown gone bad ;-), but I can't identify with the joker per se), don't hurt anyone. In short, he's a Hero anyone of us could potentially become.

Maybe the guy in the truck got lucky, or saw him get in the car and, using shortcuts, got in position to be there. The crashing of the car to save the guy gets to the core of what Bruce Wayne Batman was trying to say, protect, even if its convenient to not do so.... the accountant was an asshat, but he wasn't a bad guy, some might even say he was fulfilling his job to the stockholders by bringing to light the misappropriation of corporate assets. Saving him definately got the message across, I'm sure.

6) Cell phones as sonar...
I don't know cell tech very well, so I got nothing here ... except suspension of disbelief... billions of dollars to use for research at high tech company, i'm sure can come up with something.