If I were in the position of Robert and Stannis (and Renly I guess, but he doesn't seem to be making the decisions) I'd hold off on hatching the remaining three eggs for quite a while. The difference in effectiveness between three dragons and six dragons is pretty much negligible unless you end up fighting someone with dragons of their own. Orys is fast approaching the point where he can decide battles single handedly and with three the Baratheon brothers could literally fight the other six of the seven kingdoms and win. They can afford to wait until their children are Renly's age or even older before hatching them.
As a side note the long term consequences of the dragons being shared out like this are likely to be pretty interesting. The Baratheon dynasty as a whole is now pretty much unassailable until the last dragon dies, but with half the dragons going to the royal line and half going to others the stage is set for another Dance. That's unlikely to happen while Robert is still alive and if you didn't know about Cersei's infidelity you wouldn't expect it from the other living Baratheons either. But the bonds between second cousins are not quite the same as the bonds between brothers. Those who think in terms of the future of their dynasty are likely to be considering that very soon, if they're not already.