I think this is one of the subjects where we often talk past each other. The way I read the OP, the problem is when parts of the game becomes unnescesarily complicated. Not nescesarily that the games underlying systems are complex.
In a lot of instances, I think the games lack of complexity makes it more complicated. For instance, diplomacy and war is to a large extent decided or shaped by a complicated mix of scripted events, minigames and decisions, often with very specific prerequisites. The diplomacy system is however very simple and limited, hence the need to ‘script away’ the problems those limitations creates.
And I have to agree; a lot of the systems in this game could be both expanded upon and improved without the game becoming more complicated to play, and a lot of the added systems could be significantly streamlined, without the mechanics themselves becoming simpler or more limited.