I don't like the personal tone this is taking. We're arguing about an SF movie. Could you please back down a bit? I haven't done anything to insult you personally so far as I know.
I'm insulting the character, not you.

I thought this was clear. However the comment about "conform to your desire for them to be stupid" is basically something you've fired at many and sundry in other threads in bluntest terms.
He had no secure line of retreat or supply: his two vulnerable spaceplanes could be grounded by sheer mass of Na'vi flyers. We don't even know if there was a ship in orbit to help him out, let alone any supplies at all.
I don't think the spaceplanes made the trip alone. I'm pretty sure you don't either. The total lack of a ship in orbit is unlikely at best, since they can just leave it there (orbit's a gentle resting place) without it costing anything and loading it up until the next arrives, then send the one they've got home. Lather rinse repeat. The Na'vi are not flying things that that can move and strike rapidly. Clearing local airspace for an escape or landing should be quite possible.
He did not have enough ammunition to kill all the Na'vi out there. He could not have held his base.
He doesn't need to kill them all. The less-organized a force is, the fewer casualities are required to render it combat ineffective. This is basic tactics. Even the best-disciplined units will rarely continue to press an attack after 30% casualities, though they may reform and try again. A group like the Na'vi you have to kill relatively few of them to drive them off. Total destruction of the enemy's fighting forces is nice, but rarely necessary or required.
The base was not built on the new deposits because the new deposits had only been opened within the past few days after years of work near the original base site. C'mon, why the yelling? This makes perfect sense.
There is one, and only one, way to effectively defend something. This is to guard it. Anything else is suspect. This will dealt with later at length.
Having the whole planet thrown at him - or even all the Na'vi - would have annihilated his entire base and every person under his command.
Tactical and strategic precendent of the British Empire argues this is patently untrue. Khe Son and similar actions from Vietnam reinforce the case. Given the disparity in sophistication is even greater here, and the disparity in numbers is probably
less, I see no reason to abandon precedent.
Not to mention corporate pressure to stay on timetable, since their operation was apparently close to going into the red.
Which is more reason not to initate risky offensive actions but simply stand the watch as you were hired to.
There was no relief coming for maybe years, and possibly no line of retreat.
It all made sense.
See above precendents. Also this argues against the first point about no ship in orbit. We've come a long way from the Jamestown settlement. A Way Out is going to be more or less required when you're that totally isolated that you can't even communicate.
And, again, his plan worked. You're suffering from the Gurkha Experiment fallacy: contamination by hindsight.
Were it not for the totally unforeseeable planetary uprising his brilliant work would have been lauded as genius.
Put bluntly, this is not true. Crushing their morale as a strategy has never worked. The Brits talked endlessly about it in the World Wars, but it didn't work. Japan built their entire warfighting strategy around it after Tsushima in 1905 and lost World War II because of it. The US tried it in Vietnam and failed. It was tried again in Iraq and Afghanistan...and failed again, something the US explicitly recognized several years ago. It fails by default dealing with a force as disorganized and dispersed as the Na'vi. They simply don't have the organization to sue for peace in a meaningful fashion or to enforce a peace on their own, so breaking their morale is, at best, a temporary solution and very likely to be ineffective.
Always, always, dealing with a guerilla enemy, the path to victory has been to defend soundly. Whether it has been seeing ships to a safe and timely arrival on the opposite shore, letting the enemy shatter himself against your fixed defenses and thereby demonstrate the utter futility of his war, or ensuring basic services and needs of the local populace are met and they are kept safe, defense is, was, and always has been the only answer. One may be proactive in defense, but defense remains the only reliable, successful answer to such a strategic problem, as unsatisifying an answer as it may be.