Maximilian I said:heck, even eu2 already had problems with the napoleonic times
IMO actually the Napoleonic times were probably what EU2 best modelled. Sure armies were still stronger than in history, but this is since we build optimally economic countries in EU2 that produce huge numbers of troops (as monarchs we are most competent). Compare this to the representation of the 1419 situation - you'll find the structure of society as well as military matters diverge from history more than in the Napoleon scenario.
My point is: Think how abstract EU2's representation of the Napoleonic times is. Think of how much more specifically EU2 could have modelling that. But, if a model of for example 1066-1819 is made, can we then expect it to be as specific as if only had to model the era of Napoleon alone? The answer is question is "probably not" because there are not very many details shared by 1066 and 1819, which means the game would have to be entirely different from 1066 to 1819 anyway. But we already have that difference, and it's called Crusader Kings and EU2.
What it comes down to is decision a balance between level of detail and represented time periods. If we try to get both we end up with different models, whether we label them as being the same game or not.
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There's another strong argument for keeping smaller timelines: Game balance between player entities (human and AI). In EU2 it's not only singleplayer games that suffer from balance issues in EU2 already because of idiotic AI. Multiplayer games also tend to be out of whack by 1819, with huge monolithic nation states having formed. To some extent it's our united driving will as "virtual monarchs" which causes this issue; we run our country throughout the ages, while in history people & monarchs tend to die. Other factors of disintegrating/falling nations are simply not in the model. Thus human run country growth in Paradox games tends to be quite exponential all the way, which inevitably leads to huge differences from smaller differences in starting conditions and early happenings.