Here, so all the other threads don't get hijacked by people debating little things about the fictional movie's fictional things that bugged them (ah, nerds...)
I'll start this off by responding to the debate about the glass shielding and arrows that's invaded two separate threads here:
First off, the arrows weren't penetrating the gunships' glass at first because the Na'vi were firing their arrows at a distance. And even then, the arrows were already putting some pretty impressive small cracks in the glass. So, #1) The glass on all the gunships was probably already slightly weakened from the damage suffered in the attack on Hometree, making it more prone to shattering during the next battle (though you could argue about whether they replaced the glass or not before the second battle.) And #2 - When the Na'vi finally did succeed in smashing the gunship glass with their arrows, they were either standing on the gunships or were close enough to touch the damn things when they fired their arrows. I don't know about you, but I'd believe a 10-foot tall creature that can match the strength of a man-sized mech would be able to bring some considerable downward force to their arrow thrust - not to mention that all that force would then be focused into a very small surface area of the glass (thanks to the relatively small tip of the arrow), making it far easier to break through than if something like a mallet had been used. It'd be basically like using one of those emergency glass-breaking picks on a car window. I repeat my #2 argument for the mech glass shielding.
And yes, there can be arguments over "why didn't they have stronger glass?", or "Why did they even have glass shielding in the first place?" But I'm not going to go there, because it's a damn movie, and I don't care. You'd think the Marines would've just dropped a rod from god on Hometree from orbit, but no, we needed battle scenes - and besides, it probably would've destroyed the unobtanium deposit they were trying to mine, anyways. Paul Reiser clone wouldn't have liked that much.
And here is an easy way of saying this argument is horse shit....
IT'S SUPPOSE TO BE BULLET PROOF!
The velocity that is discharged by a gun would still be a large amount more thrust than a Navi shooting an arrow. If your argument was the case, we would simply make stronger and better arrows (and bows) and would not have to move onto ballistics.
So here is the problem, why the hell would something that is suppose to resist bullets all of a sudden crack under arrows?
And if it's not bullet proof, then why have simple glass in the first place!?! Hell on tanks not only is the glass bullet proof but they are very small windows. They might as well print bulls eyes on them, never mind that it seemed that Killgore-er-QuarICantSpellHisName seemed fine with out the glass until the arrow came that would have punctured the glass anyhow.
Then again, he also seemed to survive a ton of crap that no human could survive...which is why it was even more stupid that he got killed simply by two arrows.

In short, the bullet proof glass needed to break because like how they said in Battlefield Earth, there would be no way in hell the Na'vi could ever win. And please don't say "its just a movie" because then why the fuck did he try to do all this science shit only to have huge flaws that a six year old child could point out?
And don't get me started on the biology. As they said "MY EXISTENCE MAKES NO EVOLUTIONARY SENSE!!!"
P.S.Oh, this is one of my biggest ones...
You would think that with humans with all this tech that is a billion times better than we have now we would do something that we HAVE been doing on earth:
Stuff is below the ground. Object is on top of it. Solution: DRILL UNDER GROUND AND MIND IT UNDERNEATH, FILLING THE VACCUME WITH EARTH SO THAT WAY YOU CAN STEALTHILY MINE IT OUT!
BOOM!
No Na'vi war clusterfuck!