Hi,
I have been reading a lot on bike fit, and many people are recommending wide bars, short stem, and bars an inch or 1.5" below the saddle. I tried to get this bar height on my GF Hifi 29er, but with all spacers on top of the stem, and the stem pointed down the bars are just level with the seat in optimal climbing/pedaling position.

I know I could always get a stem with a bigger drop (and have it look very funny). But if this is the new thing, why did GF make a bike with such a tall headtube?

Some of us like level-with-the-saddle. I do.

Is it possible that you straddle two frame sizes and that you bought the larger size? As you go up in frame sizes on a given model of bike, the bars will tend to rise relative to your saddle. Go to a smaller frame size, and your bars will be lower.

You could try flipping your stem. I don't like the looks of a negative rise stem either, but flipping the stem is an easy experiment. It can't hurt to try it.

I think I'd actually prefer mine above the saddle. Just ride what feels right. Don't try to mimic other people.

Level with the saddle is actually with an ugly inverted stem already. Guess I can't do much about it and probably don't need to, just wondering what GF's reason for making it so high was.

I like my bars to be right around the same height as the saddle on my Trek. It looks odd, but feels great.

I looked at a geometry chart and even the XXL has only a 145mm head tube. I have the opposite problem, I can't find a bike with a tall enough head tube. I may go try an Epic, supposed to be 185mm.
I've also found that some makers don't increase the head tube length in the larger sizes, the top tubes just get longer.