Regression slopes and allometry

Hansen et al. 2008 left me feeling somewhat unsure about the possibility of estimating the optimal regression slope from comparative data. Although their method partially accounts for maladaptation, their simulations suggest that slopes will still often be underestimated (though they think this may be partly an effect of the topology of the primate tree they tested it on). I think that in many applications the value of the slope will not matter, but in others such as hypotheses about allometry it could be important. Is the timescale of adaptation fast enough that this isn't a problem? Are there better ways of calculating allometric slopes?