I'm only about ten episodes into RahXephon, so I can't say much about the ending. It's interesting so far, however. It manages all of the surreal and bizarre elements very well and integrates them into the story nicely. In fact, it probably does this better than Evangelion, which could get sort of rapid-fire in its introduction of psychological and theological symbolism (which was never really explained or elaborated upon). RahXephon isn't as thematically deep as Eva (at least, not yet), but it paces itself much better (so far). I can't really comment on how comparable the characters are yet, because there hasn't been much development in RahXephon so far. Though, I don't really think that Eva had quite developed (read: emotionally wrecked) it's cast this early on either.
And, I actually think that both the last two episodes of the Evangelion anime and End of Evangelion sort of define the series. If they were traditionally comprehensible, it wouldn't have the same impact.