In Rav Sadiaa Gaon's prayer book, he lists a short prayer for before and and after baths. Why isn't that said anymore (I'd assume it was said in his time)? The text I'm referring to can be found here: http://www.hebrewbooks.org/pdfpager.aspx?req=20685&st=&pgnum=148&hilite=
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Saadia Gaon didn't innovate it. It is based on Berachot 60a:
Except Saadia Gaon's formulation is more explicit about the danger: "Blessed are You, O God, Who has saved me from the fire."
Given this, there are two obvious answers:
1) Are you in danger from fire when you take a bath? Their bath houses are not the same as our bathrooms, such that the formulation of the blessing, and indeed, the very reason for the blessing (the danger), is uprooted.
2) Even in the gemara, Abaye argues. While Saadia Gaon evidently held one way, perhaps other Rabbinic figures held otherwise.