I definitely don't think you're alone there, and yessss I know the chorus of "But the Compilation has now established that..." is on its way, but I will say that I, for one, LOVE the ambiguity of the original ending and would be so pleased to see it carried through faithfully. We know that Cloud has finally figured himself out, that the Lifestream has surged through to aid Holy, the clash is happening in a blinding flash, and the rest? ...Is up to the Planet (and to some extent, the player). As Bugenhagen asks earlier, is Man inherently a danger to the planet? Are we bad or good? Will we be wiped out in the Planet's defense or spared (with clues sprinkled about)? Such a bold move for the often cut-and-dry world of videogame narratives.
That said, I wouldn't throw a fit and break my toys if they decided to make a more definitive, tie-up-the-ends ending, especially if the journey itself is handled excellently. It's just what I'd hope.