Given TTGL's themes and Gainax's tendencies, I'd say the beginning sneak peek was never a bad ending. I'm guessing they originally went for a "alien empire decides to invade earth to expand their empire, Simon and crew lead earth's army against them ala generic super robo vs alien series, fucks shit up" approach. And then decided to expand upon the theme they had going with Lord Genome and Rossiu's village with antagonists and logically unavoidable injustice instead of going down the "OMG ALIEN EMPIRE INVASION! EVERYBODY OUT THERE'S AN ENEMY!" approach in an attempt to look deep.
Oh, and they made suicide attacks and some of Japan's more idiotic actions throughout their history during the past 100 years look cool during the process. As awesome as fighting to protect your homeland is, suicide is moronic from a fighting standpoint. Attacking knowing you'll make a difference? Fine. Attacking knowing that it'll do absolutely nothing? Stupid. Not to mention it's a disgrace to the people who actually died because of the kamikaze raids. Aside from nutcases who thought they'd become heroes, almost everybody on a Japanese suicide mission during WWII was crying for their lives at some point. While a large number of people who were against the tyranny and abuse by the Japanese government and extremist right-wing morons was forced into the army, killed by soldier and cops, or shoved into a jail cell..
Of course, the movies probably reduced the suicide count and boosted the "fight for our lives, fight for our friends, oppression is wrong, let's be friends and make a better world" image, but still, I honestly doubt the bad end was really an alternate future. Gainax isn't smart enough to add real psychology to their series, personally.
Then again, this is Japan we're talking about. As awesome as some of their shit is, they have a lot of morons running their systems. Morons that are on par or worse with Bush Jr. at times.
