Hi,
It depends. The AIC just measures how well the model fit the data. A model that uses more data (e.g. more information) is bound, by and large, to do always better than a model which is applied to data with a lower information content (such as, missing data).
The Bayesian Information Criterion might be more suitable as it adds a penalization in terms of the available observations. Thus a model that uses more data is equalised in some way in comparison to a model that uses less data. That said, BIC is reliable if you have observations well in excess of the model parameters and you are not dealing with high dimensional problems.
There is also another criterion, the Deviance Information Criterion, that generalizes the AIC and BIC to hierarchical models.
To sum up, I would think that BIC is a better benchmark to judge the relative merits of the two models.
Regards,
Giulio