The engine is just plain hard to make maps for. The Hammer editor, although robust, is harder to learn than most games. Couple it with the fact that the maps used a technique called Binary Space Partition to break up the levels. It had the advantage of running fast and looking good but any minor mistake in developing your map could lead to ‘leaks’ where a portion of what should be inside the map accidentally opens to what should be outside the map, and makes things run horribly or not at all.
Tl;Dr it was difficult to develop for. Putting in the time could lead to great rewards, but other engines were just plain easier to learn while offering the same or better rewards
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