Well, i would say troubles in mid-game occur due to screwed-up start.
If you lose few early battles (or even win them with Pyrrhic victories) then you will face slowing of your Empire expansion and BIG problems later (e.g. you have recruited a bunch of mercs and they have failed to take some city in order to loot it and cover the bankrupting budget). I have abandoned one of my campaigns because of that (Hungary h/h). Later you just do not have enough money to build up your trade, since all your neighbors wage war against you (because you failed to finish them off early) and all your money goes to recruiting everything you can get...
Just my IMHO, it has been so in my games for England, Spain, Hungary and HRE (especially for last one, since it was played on vh/vh ). Not sure if it is true for factions though...