I suppose the procedure to target embryos directly would highly compromise the viability of the embryo itself. Alternatively, ES cell lines which has been thoroughly tested for stability in culture can be obtained in high enough numbers, transfected and then evaluated so that only those viable and with the transgene in place can more or less safely be transferred to an embryo were they will integrate as germ line when they are in the niche (and therefore redirecting cues) within the inner cell mass.
It simply is due to the number of cells required for homologous recombination (HR, or gene targeting) taking place when you either inject target vector into pronucleate embryos or electroporate mouse (m) ES cells. A superovulated female mouse can provide around 20 injectable fertilized embryos. To make HR occur, you need millions of embryos that is a fortune, not to mention about animal sacrifice required for embryo transfer, breeding and maintenance of the animals until the appearance of positive HR. Impossible to support the research!!! However, it is a piece of cake for totipotency-proven mES cells to make that number with little cost in a few days.