The animal model, with all its power, can do little to overcome the effects of genotype by environment interactions. If sires really do rank differently in different regions or management systems, the only way to fairly compare them is on a within- environment basis. This would mean separate evaluations for each environment - a solution which may not be practical. The animal model has only modest ability to reduce the bias caused by preferential treatment or inaccurate data. No model can overcome the problem of bad data.
All genetic models depend to some extent on quantities which can only be estimated.
Even the simplest breeding value calculation, for example, requires an estimate of heritability. Because of its multiple trait characteristics and unique way of handling maternal breeding value, the animal model relies on a number of heritability and correlation estimates. It is particularly vulnerable, therefore, if these estimates turn out to be inaccurate. The biggest problem with the animal model, and the one which has so far prevented its implementation, is computational difficulty. Applying the animal model to a realistically large set of field data is a computing nightmare.