Amnesia wouldn't be the same, if the story is fully reveiled. It is supposed that the story you experience is a collection of memory fragments, thus keeping you in the dark basically and leaves certain aspects open for speculation.
It keeps the game interesting, look at the Half Life Series, in their story there are also certain parts which arent reveiled, like G-Man for instance. Same with Amnesia, it's supposed to be that way, so the talk about the game stays interesting.
I think the monsters are some sort of fleshgolem, Alexander controls to kill Daniel, because Alexander is afraid Daniel will interrupt his ceremony. At one point he gets captured by these "Brutes", they didn't kill him there. But these creatures are designed to kill, they are the guardians of Alexander while he is vulnerable, the water monster could be an anomaly, which occured during the experiments with the Brutes. They could be just energy. But i'm going too far already