A lot of the time, a game has the "getting bigger causes problems" mechanic, like Chris talked about, not because it was intentional, but because the developers have handled macromanagement badly, or failed the design in some way.
Even AI War is guilty of this to a certain degree with the current pathing mechanics. When you own 12 planets all over the galaxy, and are trying to spread your forces between them, having to give them all specific commands with shift queues on how to reach their destination can be painstakingly tedious, and one small mistake can send them through a dangerous world accidentally which will cause a disaster or even end the game.
There's a fine line between mechanics which really challenge the player to overcome himself, and which are just bad coding. Luckily, the best developers like Arcen stick around long enough to make sure the former stays and the latter disappears
. Most developers leave their games half-baked, and that's the sad truth of the industry.