Well, the game set up is an approximation of the situation in 1080, and some of it is just wrong - like Crete. Curiously most of it was right for M1TW, but I guess CA wanted the game to be more balanced between each faction. It's pretty good as it goes, but there might be a mod that puts a lot of these right. Many of the mods add places and factions shown as rebel or missing from this game. CA have given people the option to mod, and someone else might know of the most historically accurate.
The problem then is to keep a balance - how do you make the small states strong enough, and the empires "weak" enough. They also responded to opinion on the forums that, for example, wanted Portugal to be a playable faction from the start. Another issue is that boundaries were so fluid that it makes a difference even if it was 1078 or 1082 (e.g. Durazzo was Byzantine, taken by Robert Guiscard, Norman Duke of Apulia in 1082, regained by the Byzantines 2 years later from Bohemond - later Prince of Antioch - the son of Robert Guiscard).
The empires are misleading, of course. Byzantium was internally divided and fragmented. The HRE was a collection of kingdoms, dukedoms, nobles etc who were often at war amongst themselves, and wouldn't let the Emperor have enough money to go conquer Europe. As you drill down into the situation it just gets more complicated, e.g. the English King was also Duke of Aquitaine and Anjou (as well as Caen/Normandy), so should have control of these territories too, BUT, they were separate titles from his title of King of England, and he was vassal to the King of France for those places. The French King at the time was too weak to run France as a nation state.
The games designers have made lots of places "rebel" that weren't.
So very broadly here's a few:
- Bordeaux/Aquitane should be English
- Angers/Anjou should be English
- Dijon/Burgundy in 1080 was part of the HRE (though part of it was French)
- Marseilles/Provence in 1080 was part of the HRE
- Genoa was a separate state from Milan, and independent
- Milan should be part of the HRE (or rather the Emperor was also King of the Lombards, as a separate title)
- the HRE should have a port (Trieste) between Venice and Zagreb.
- Hamburg was part of the HRE
- Antwerp was part of the HRE
- Zaragoza was part of the Kingdom of Aragon
- Toledo was taken by Leon/Castile in 1085, so not yet in 1080
- the Amorovids (Moors is a European word) ruled Morocco and Cordoba
- Sicily and Naples were separate states (though ruled by the same family of Normans)
- the Byzantines still had fortresses in the Naples region in 1080
- Durazzo was Byzantine in 1080, but lost to the Normans/Sicilians in 1082, and regained again
- Sofia/Bulgaria was ruled by the Byzantines in 1080
i- Trebizond was Byzantine in 1080
- Jerusalem and Acre were Fatimid Egyptian in 1080
- Antioch was Byzantine till 1078, then Armenian for 6 years, then Seljuk Turk in 1086
And so on. If you consider Portugal to be the County of Portugal, rather than a kingdom, it works
Someone might post a really historical mod, if such a thing is possible ... there's no good date to fix as a start date ....