Ray, I find your nerdy-nitpicking to be kind of endearing, to be honest. Dude, there are a MILLION reasons to not like "Avatar", but the ones you chose to highlight actually just make it look like you've never really paid attention while watching this movie.
These are films about "What these jack@sses did in that situation", common effing sense be
- An explanation that Jake was picked by the company because as a twin he was a genetic match to his deceased scientist brother - followed by an explanation from scientist Norm Spellman that the avatars are grown during the five year voyage to Pandora. Umm... doesn't Jake already have his brother's avatar waiting for him at Pandora? Genetic match? The reason we're switching jar head Jake for scientific Tom terrific?
- Exactly what was it the company was going to pay a lot to "Jake the grunt who dissected a frog once" to actually doooooo when he got to Pandora?
Jake's brother has never been to Pandora. Nor has Jake's brothers' avatar. Jake's brothers' avatar IS Jake's avatar. That's why Jake was picked. Because they spent all this money developing a new avatar (on Earth), for Jake's brother. But then Jake's brother died, and they had this expensive baby-avatar with no human pilot. Oh, wait a minute, Jake's brother had a twin -- Jake! So they are able to use Jake to pilot the avatar that was originally intended for his brother. The avatar isn't made from scratch, during transit, it just matures. But it was created on Earth. There was no avatar waiting for Jake on Pandora; the only avatar that he could use is the one that traveled with him, from Earth.
And it is very clear what they wanted him for. On the surface, they thought it'd be neat to have an avatar that is highly trained in security (they've already spent all this money on the avatar, might as well bring along the grunt who fits the avatar). Beneath the surface, they just wanted a spy. Send in a jarhead to hang out with all of the scientists, under the auspice of security, but report back to the military guys. The fact that he was taken-in by the Na'vi was serendipitous.
And now that I think about it, if the Na'vi clan was already familiar with Dr. Grace Augustine's avatar through her assorted schooling efforts wouldn't they also be familiar with Jake's brother's avatar? But they act like they've never seen him/it. And being twins, wouldn't a new "Jake avatar" look pretty darn close to the "Tommy avatar"?
No, like I said above, Tommy had never been to Pandora, nor had his avatar.
Sheeeeeeeeiiiiiiiiiiiiiiit!