This was the big limitation that effected Monarchs historically. Imagine if Edward the Third was able to keep his vassel levys in the field for a decade. There would never have been a Hundred Years War.
The fact is for extended service Lords were obligated to pay for thier vassals levy. In the book, A Distant Mirror for example, there is some clarity shed on this, in which King Edward agreed to pay a set rate for each type of liegeman. A Knight was paid X daily, a Knight Baronet was paid X, a Count whom brought 30 men was paid a set rate according to what equiptment these men had. To pay for food, horses and so on.
And yes, the 90 limit is frankly what made campaigning seasonal. To get beyond this a Lord needed to have deep pockets. Edward the Third resorted to all sorts of clever devices to raise money, and this caused him all sorts of domestic problems.
THIS WAS the greatest limitation of the period. Remember no professional armys existed as we know them today. Some citys hand a trained levy to protect it, as did nobles with professional retainers that did nothing but practice the art of war. Those personal retainers or the nobles personal levy was a fraction of the forces employed in the war cited above. This is also why Mercenarys became so prolific during this period.
Okay, I'm going to refute some of what you said, simply because as much as Tuchmann is a good starter read she gets some of the military history aspects wrong because her focus is Anglo-Norman (for laymen: English). England and France are aberrant in the period. In the sense that vassal levies were paid for by lords, on the continent they were still using the fedual levy where the vassal provided service to the lord OR payment in lieu of. Also what made campaigning seasonal wasn't the 90 limit, it was LOGISTICS. It was seasonal because there is a limited window in which one can fight in armour in Europe without either trashing the armour or yourself. Add into that getting your Knights, their retinue (at least 8 if not more like 10 retainers), a slew of horses, and of course the basic necessities to feed and bed them around was a daunting task in an age where you either traveled by horse, or by boat.
The greatest limitation to warfare in the middle ages (as it was to Rome and is today) was getting the warfighter to the battle in good health and well nourished. Since the medieval army was dependent on the land there was a lot of raiding ("razzia") tactics and scorched land. Tuchmann addresses this in the fact that western France basically got trashed by the hundred years war because of the constant raiding. If you read more about the Northern Crusades you can see that as "invincible" as the Teutonic Knights (ahem a "professional army" of its day) were, the Lithuanians realized than an all powerful Crusading Knight is really pretty easy to kill when he has to eat his horse or starve in hasty retreat in the dark woods of Prussia and Pomerania.
My only complaint with the game (other than the fact that levies get spun up and disbanded way too easily), is that I can march my Saxon army through Luebeck and into eastern Mecklenburg with minimal to no casualties (EU3 was better about losing forces this way). Add to the fact I can do that in December/January (the march I've mentioned was notoriously treacherous and stark in winter time) and yes the combat system isn't highly realistic.
All that being said, I agree that the familial structure is too cutthroat, and I wish there was a tag or attribute that was added to the Dynasty to mitigate/reflect the fact that some dynasties were out to get each other (the Angevins for instance), while others were more tribal/communal the (De Coucys or William Marshal).