As we have learned, the original institution of the Sages was to bless and give thanks for each and every act immediately upon enjoying it: as one wakes up, she thanks God for the soul He placed within her and says Elokai Neshama; as she opens her eyes, she recites, Poke’aĥ Ivrim; as she stretches her limbs, she recites, Matir Asurim; and so on with all the blessings in that manner. However, today the custom has changed and we recite Birkhot Ha-shaĥar consecutively.
Why did this custom change? It is obviously more appropriate to thank God immediately upon enjoying His bounty. In that way, the process of awakening attains profound significance, as blessings of thanksgiving to God accompany each and every stage. Indeed, Rambam rules that all Birkhot Ha-shaĥar must be recited exactly as mentioned in the Talmud, each berakha at its appropriate time. There are some Yemenite Jews following this ruling even today.
However, as noted, the prevailing custom is to recite all Birkhot Ha-shaĥar at once. The reason for this is that if they are recited in the process of waking, there is concern that one berakha or more will be forgotten; however, if they are recited consecutively, it is more likely they will all be remembered. Moreover, we want to enhance the mitzva and recite Birkhot Ha-shaĥar in the most respectful manner, that is to say, with clean hands and while properly dressed, and therefore we delay the recitation of the berakhot until after all the preparations for prayer are finished. Furthermore, some people find it very difficult to concentrate immediately upon waking up, and only after they dress and wash their faces are they able to recite Birkhot Ha-shaĥar with kavana (based on SA 46:2 and Seder Ha-yom).