I didn't understand the Gainax Ending to Contact until I read a critique of Flower, Sun and Rain. The point is this: All the characters in the game are stuck playing the roles that the game forced upon them. The "villains" and "heroes" aren't really enemies, or even heroes and villains at all. Like actors in a play, now that the game is over, they stop fighting and go back to their normal lives.
Due to the parallax effect and doppler effect it would have been impossible to fake a signal from Vega, thus rendering the "you imagined it" ruse laughably bad. Of course, Ellie does say it's impossible. Kitz insists it could happen, but then, he is a politician. He believes that Hadden had the resources to pull such an "elaborate hoax".
There would also be evidence inside Elle's body. Food moves through the digestive tract at a fixed speed, and blood sugar declines predictable after the last meal (which is why you get hungry). She would have been given a medical examination of some sort just before and afterwards. In many ways she should look 18 hours older.
And the strange and unexplained industrial light and magic show when the rings are activated. After all, if 'nothing happened', why did the whole thing look like the Bajoran wormhole?
There's also the fact that the machine altered gravity in its vicinity during the build-up to activation. Do they government really expect people to buy the idea that Hadden came up with anti-gravity technology to make a hoax look really cool?
Another example (from the movie): why can't they just run the machine again and send another trustworthy person? The machine in Japan was undamaged, the pod was undamaged, they know it's (relatively) safe... it just needed refueling. Hell, it would have been cheaper than the international tribunal they end up with!
It's explained at least in the book that the aliens were closing the wormhole link for a while, so they can't send someone else for some time. Inevitably they'll keep researching into it and eventually make another trip; that part is just not in the story.
Ellie asks Palmer if he's heard of Occam's Razor. As a divinity student, Palmer would know what Occam's Razor is. He says "Hack-Em's Razor? Sounds like a Slasher Film." But he doesn't say he's never heard of it.
Some of Ellie's outfits. When she first goes to Hadden Industries, she's dressed in a turtleneck and jacket, similar to how Carl Sagan often appeared. When she is testifying near the end of the movie, she is wearing a maroon dress, colored similar to Hadden's suit when they first met.
The very odd visual effect while Ellie is in the transit system which makes it look like she's being stretched one direction then propelled at a very high velocity in the opposite direction left this viewer overwhelmed by Narm for years. Until I realized that even real spacecraft use the ''slingshot'' effect.