Personally, I think its because they weren't sufficiently tied to difficulty level. Difficulty levels were focused on blunt hammer things like more starting warriors and more starting settlers, instead of on smoothly-graded challenges that apply throughout the game. Meanwhile unnecessary challenges were applied to lower difficulty levels, where they aren't needed or valued.
Some people like to kill everything, some people like a relaxing game; those players generally do not want anti-snowballing mechanics and shouldn't be forced to put up with them. Mechanics that limit growth, make expansion more challenging, make maintaining a tech- or military-lead harder - those are all things that belong in higher difficult levels, for players who don't want a "win your way" game, who instead want a "maybe I can win, maybe I can't" game. But they shouldn't be in lower difficulty games where they just annoy, frustrate or limit the player from playing the type of game they enjoy.