Rav Reem HaKohein, the rav of Otniel, has written an interesting psak in a shabbos parsha sheet article.

The topic is the current hot issue of brain death and what is considered halachic death. There are some rabbonim who consider brain death to be the time of halachic death, while there are some rabbonim who hold brain death is not death but cardiac death is the halachic point of death. The ramification of the debate is at what point can one in such a situation possibly donate organs.

Rav Reem Hakohein is a proponent of organ donation, and he holds that brain death is halachic death. Rav Hahohein paskened in his article that one would not be allowed to daven for the recovery of someone who is brain dead. The reason is because once one has gone through brain death, there is no recovery. Rav Hakohein adds that even according to those opinions that are machmir to not call it death until cardiac death, and that one could not donate organs after brain death because the person is still technically alive, one still cannot daven for the recovery of a brain dead patient.

And the reason is because davening for such a person would be a tefillas shav, a prayer in vain, which one cannot say. There is no recovery from brain death, and therefore one cannot daven for such a recovery. Therefore, irregardless of whether or not you hold brain death is halachic death, one would still not be allowed to pray for the recovery of a brain dead patient. (source: ynet)

I see no reason to say person could not daven for the patient in other aspects, that he should not suffer, that he should pass quickly rather than languish, that he should have merit in shamayim, etc. The only problem is regarding praying that he recover, which is impossible.