A few of the big things here that aren't historical:
1. Attacker and defender attrition are imbalanced. In EUIV you have a huge stack in one of your provinces, I have a huge stack in one of your provinces. I take siege attrition, you sit there with nothing. The single biggest cause of attrition in this era? Disease. Does it give a rat's ass about which side of the border a big unsanitary nightmare of a armed camp resides? Nope. Well what about other forms attrition? Desertion, well that get's iffy it was easier to run away nearer to home (you were more likely to speak the language and you likely had some family contacts somewhere to hide you) but you had more reason to run away in enemy territory (if you were losing, not dying is great motivation). Starvation generally favored the attack during maneuvers and the defenders during sieges. On the move you can pillage enemy peasants to the bone - slaughter the draft animals, eat the seed grain, and even rip up trees to eat the roots (though I can't think of a time that was done when you weren't already mostly dead). Doing this dispoiling on your own turf means you pay for it - either you end up paying the bill directly or your tax revenues fell as your peasants had less money (thanks to having to replace the foraged items) or simply were dead (and generally dead men paid few taxes). On defense, normally cities were better about having large grain stockpiles and most fortified locations tried to command either roads or more commonly rivers. Moving grain overland to support a siege was expensive as heck and hard. Moving it down rivers was easier and the guy who controlled the fort with the guns had a decided advantage using riverine craft.
2. This is turn leads to one of the most glaring inaccuracies of EUIV warfare: rivers aren't worth a damn. Yeah you get a bonus defending behind them. That's pathetic. Look at every major campaign in Europe notice how some ground is constantly tread over, notice how people do really weird non-straight lines. That is because they are following river courses. Moving artillery was a bear. Moving men, also hard. Wagons? They ran into a nasty, nasty rocketry equation where you need to bring fodder. But that means more wagons, meaning more horses and in turn more fodder. Enter rivers. Rivers were 10x as cheap to move goods and often multiplicatively faster as well. Why could the Ottomans field so many more men and artillery pieces in the Balkans than in Persia? Because the Danube is the equivalent of a twelve lane super highway while the Persian front tended to lack anything better than a two lane dirt road. Virtually ever major maneuver from the EU period makes no sense without rivers giving faster movement, better reinforcement, and vastly more timely information (as over long distances rivers could make far better time than horseback riders). Likewise, if you were going to ship food in for a siege, there was an outside chance you might be able to feed the siege camp from the river. There was virtually no chance of moving food more than six days march overland.
3. Wars revolved around territory. Yeah some wars were decided by annihilating the enemy army, but they were rare. More often you wanted to take territory, garrison it, and possibly bait the enemy into a fight. For much of the era, armies could decline fights for a long time - so you either pillaged and burnt the place until the king defended his people or you took some place valuable and either made your demands in exchange for returning the place or just kept it instead. In a long campaign you might have only a single siege - but it would be of somewhere important and everyone would come to the table - because it falling meant the enemy couldn't relieve it and more such sieges were quite likely. If somewhere you owned was under siege and you just let it fall without a fight, well the locals might decide they are better off under new management and other strong points might not be willing to hold out while starving later.
4. Artillery in the early period was far more about morale and shock (not as defined by Pdox) than about gunning manpower down. Cannon are great at killing people in late era, but early on firearms and cannon just broke the nerves of people opposing them. We take for granted in our world that things can be propelled at insane speeds easily, that blinding lights happen at any crappy disco, and the deafening sound just kinda happens when people drive buy with too expensive of stereos, in the EU era, that just wasn't possible. For a lot of non-professional soldiers, the first time they might have seen anything like a cannon going off would be when the guy next to them gets ripped in half by a cannon ball. There are no movies, few paintings of this even exist, and descriptions just don't do it justice. This is particularly bad when you look at the effect of artillery on less militarily proficient armies. Take the Chinese against the Dutch in Taiwan. The Chinese set up their cannon in range of the Dutch with no defensive works. The Dutch fire through the night (hitting little), in the morning they can finally aim and fire into the army surrounding the Chinese cannons. There is a brief slaughter of manpower at the guns - and then the army breaks and runs out of cannon range - leaving the dead, wounded, and the so terribly precious cannon behind. Eventually, yeah the artillery became great infantry killers, but for a lot of the EU era they broke morale more than they actually killed people.
5. Heavy cavalry was insanely good and insanely expensive. Now there was terrain where heavy cavalry sucked, but the average Polish heavy cavalryman could ride over a Janissary with ease; most Janissaries choose to buy reasonable firearms and only the most unwieldy firearms could punch through heavy plate. Archers and crossbowmen also tended to do poorly against heavy cavalry. On the plains, the Poles really were absolutely freaking terrors against just about everyone until the Swedes made it big.
6. Which leads to something alluded to earlier in the thread - troops at the same technology level were very different. Hussars cost a fortune, but on the plains they can destroy infantry. Line infantry (e.g. Wellington's troops) were expensive, but devastating at fire; column infantry were cheaper and crappier at fire, but they were much better for shock actions. Right now every troop type for a given technology costs the same and there is jack all you can do to effect the quality of your troops outside of national ideas, in reality you could opt for highly trained profesionals, exceedingly expensive nobles and their retinues, or impressing all the rabble who can light a match. This also allowed you to better match your troops to your terrain.
7. Wars were not death matches. Even against heathens, heretics, or "atheists", very few states became dead enders. If you lost one big battle, chances are you would lose more. Nations were vastly more willing to lock in their gains or cut their losses than in game. This is really bad, if I have to effectively kill the Swedish army to take Skane, why not hit it just a bit harder and siege a few more provinces to take all of southern Sweden? The whole peace system has gotten backwards and is showing its age. In this time period prolonged wars faced diminishing returns, but the engine makes them effectively increasing returns affairs (to long before you can take any real gains, to short before you can take maximal gains) and frankly makes it better to go big in one war than small in two or three.
8. Up until, maybe Frederick the Great, reinforcement armies rarely accomplished anything after the battle was joined. It isn't really until Napoleon's logistics that you had controllable method to march armies a decent bit distant from each other and then join forces after the battle was begun. This had profound effects - this made fortifications vastly more important - as you could shelter in those until reinforcements came. Likewise, your invading armies were limited in size - they could only manage so much frontage on the march before the left and right became unable to support each other; however smaller frontage means less farmland to pillage and hence smaller armies you could support.
Which leads me to my last issue. Everyone and their brother has a suggestion about introducing supply lines in some complicated fashion to EUIV. This idea needs to die. Supply lines as the concept currently exists did not exist until the very tail end of the era. Armies in this period needed food, shot, powder, money, and maybe clothing. If you took every wagon in the Imperial army, you couldn't make a dent in the food supply. Armies on the march between battles were pretty much self-sufficient. You need food? Rob a peasant. You need money? Rob a merchant. You need shot? Rob a church. You need powder? Rob a magazine. You need clothes? Rob anyone. It really was the case that armies ate off the land, they recast their (and the enemy's) shot with a small bit of lead bought or pillaged. Powder was about the only really dear military supply, but you only used it when you fought and you could often buy it wholesale in enemy territory or just loot it from captured arsenals. But what about "lines of communication" those were pretty much what it sounded like - they were paths to and from the rear down which official information could travel. Given the snail's pace of news in this era, communication meant the difference between knowing there was a peace and fighting a completely useless battle (sea New Orleans, battle of). Getting cut off meant you had no more pay coming up from the rear (so it was really pillage or die at that point) and that you could blunder into anything - like say your French enemy's new Spanish ally. Fortunately, this, above everything else would make EUIV unplayable. You have instant access to all information in your empire and you can instantly recoordinate your troops everywhere in the world. Ditching this instant communication would be hell on the AI, so I vote to keep the cellphones in the 15th century. But this doesn't mean we should import Vicky era supply lines into EUIV.