Have you ever tried Magna Mundi for EU3? There you had to plan some things 100 - 200 years ahead of time.AE, OE, manpower. Waiting game.
Anyway, thats why its called Grand Strategy: Your action have long term impact and may come back to haunt you even after several decades / hours of gameplay.
It is certainly annoying from time to time to see your expansion being hampered by these game mechanics, but thats part of the game.
In real live nations can take decades to recover from a war or to smoothen bad relations with their (former) enemies. Thats part of the game.