i dunno man, my 29'er hard tail has a .2" shorter stay than my 26" trail bike (16.8 vs. 17.0)This feeling never really goes away. I think because the BB is significantly lower than the rear axle and the bikes inherently have to have a longer chainstay, they just don't pull up easily.
once you get a slacker head angle (69 on my hard tail), a short stem (65mm) and wide bars (30.5), its like riding faster more stable dirt jumper, not a clunky POS.
obviously getting a FS 29er under 17" stay will be more challenging.