To the OP: What you originally posted wasn't problems with the game mechanics... It's more of you being a sore loser. People get screwed over all the time, like having your genius son get maimed and die, leaving your poor content and craven son to inherit. This is can be fun or frustrating.
But here are a few things that I think PI has so far improved, made worse, and/or could use improvement.
-Crusades: Originally, Crusades in the game was a big mess. People had to individually declare a crusade on the target, none of which were allies so all the armies were scattered and weren't united. The Fatimids could easily pick off each Army individually because they weren't considered in a joint stack. Also, the Crusade will never end until someone wins. Now, Crusades is a joint effort led by the Pope and acts as a single war, making it challenging for the defender. But there are still some problems with crusades. For example, whoever wins the crusade gets the Kingdom. A Frank became King of Jerusalem in history, but instead we'll see France plastered over the Levant. What could be improved are emerging states, such as adventuring sons like the d'Hautevilles in Sicily.
-De Jure Drift: Pretty neat feature if you ask me. But it won't work if you hold a Kingdom title corresponding to the de jure duchies you want to drift. You have to destroy it to make it happen. Would be nicer if you could drift everything under your main title. Another problem is drifting unconnected pieces of land. Usually I see Bohemia in Italy due to a marriage. Drifting should be limited to adjacent duchies. But the timer can still move on, but will stall being incorporated to the Kingdom until a newly acquired duchy connects the base Kingdom and prospective duchy.
-Vassal-Liege Contract: Not talking about how the King of England should also be the vassal of the King of France should he have French lands. No, I'm talking about titles and their lieges. Below Medium Crown Authority, vassals are allowed to make war on other vassals. As a liege, I don't like this, but I think it's fair. But what I don't find fair is the Duke of Anjou declaring war on the Count of Vermandois, my vassal tied to my title as Duke of Valois. If you click on Vermandois, the province, you will see that it goes from Vermandois > Valois > France. This means Vermandois is a vassal of the Duke of Valois, while the Duke of Anjou is a vassal of the King of France, both of which are me. If Anjou wants to declare war on Vermandois, then that should be a traitorous act, because he's declaring war on me. Why is this so important? Well, if you look at the HRE, the Emperor is always screwed. Duke of Bavaria always spent his time defending his Counts from rival Dukes. But now that he is elected Kaiser, all of those Counts are fair game, he can't do anything about it even if he also holds the Duke of Bavaria. And then, his successor does not succeed him as Kaiser. He loses those vassals. Some more on vassal-liege contract, you also lose Counts as vassals if you are elected as Kaiser. Let's say you are Duke of Bavaria, and you have the Count of Tyrol as a vassal. You do not hold the Duchy of Tyrol. You get elected as Kaiser. You don't get elected again. The Count of Tyrol is no longer your vassal. See the problem here?
-War: The best way to make the war system most ideal to me is to scrap it and incorporate a Campaign mechanic. Instead of ordering around armies and moving them province by province, the war would act independently. What you do is you select someone to organize the campaign, probably you or the marshal, and you set the funds to run it. This is probably a fixed expense, the more you spend, the more effective the armies will be (the fund goes to numbers and logistics, all of these abstract things.) Martial can effect how much you spend, good Martial would require less money to achieve the same effectiveness with someone with lower Martial. You can alter the funds at any time. With this campaign system, you don't have to worry about moving big numbers across the map. And it could allow much smaller Kingdoms to take on bigger guys. This way, Abyssinia could actually survive. Egypt would have to invest so much money to even get troops across the desert, most of which would desert. Once the Egyptians arrive, the Ethiopians would have already assembled their levies (Do you guys have any idea how long it takes to do that in Abyssinia? I think this is the reason why the Ethiopians always die.) It would probably be complicated in math, but very simple on screen. You select someone with great martial to run the campaign, he might make good choices, he might make bad choices. There might be events during the campaign, but I think the player should have less control on the campaign running (i.e, move troops here, plant them here, stack them up, etc.) and just have the AI do its math. The player is smart, and with this campaign system that I believe would never be implemented because it's just so different and requires a lot of overhauling that isn't necessary, I think the AI and player would be on equal terms in warfare.