We can agree on the idea that countries should make you feel like they have had a previous history. There is
another thread about this.
But there is a difference between accurately showing the situation countries were in in 1337 and extrapolating their future.
Having the 100 years war be ongoing in 1337 is fine. Having a specific situation in which the Byzantine empire is heavily indebted and stricken by inflation in 1337 is perfect. What isn't is planning the war of the Roses, the Partition of Poland, the rise of Prussia or the Mughal ascent centuries in advance.
As I said earlier, it is fine to plan for ways to make events resembling those happen, and to, in the event that those happen to the right countries, have historical flavour in the form of texts and historical characters, but those events were very contingent. As an example, had France not bought Corsica from Genoa, Napoleon couldn't have become french emperor.
I can understand what you want. Years ago, I asked for a slider of historicity for EU. I eventually realized that history was a lot more contingent than I initially thought. Thus, in a game made of thousand of ticks, each of them susceptible of derailing history (and often doing it), I don't see how beneficial it is to insist that history should happen as it did.
But that's setting your position at an extreme. Of course you don't want a graphic novel about the history of the world. On my side, I don't want the game to feature bland countries either. But I want their difference to come from their (past) history, and the ability to change their makeup with time. This is hampered by TAG-based mechanics such as mission trees.
Imagine as France you started with a privilege to the nobles which says the nobles have more castles and thus that grants you a bonus to cavalry (completely made up, I didn't look at the actual unique bonuses countries get and don't care about them). What would prevent Flanders to get a similar privilege, coming with its advantages and drawbacks? Only, they wouldn't start with it, so they would need to make big changes to their country before having access to it. This would have its own opportunity cost. (I'm steering far away from the topic of MTs, here, though, sorry).