Great concepts but many loose ends.

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The ending was an anticlimax - all three of them.

Yeah, I think many people feel that way. The endings were okay in my opinion, but a bit of a letdown after all the cool buildup that came before.

Absolutely super graphics.

Technically, they're kinda outdated. Aestethically, they're great.

Although the choir was a visual masterpiece the trough in the middle made no architectural sense.

Well, it made sense for gameplay. (Bridges give the huge room structure, thus help player orientation, create bottlenecks where the level designer can be certain that the player has to pass through and create areas where the player has to be even more cautious due to lack of room to flee or hide) Sometimes gameplay is more important than super-realism I guess

Pity we never see this shadow thing that is threatening even in the end game.

You see the shadow all the time, right from the beginning. It's the red stuff coming out of the walls. (or at least that's it's physical representation...sort of)