Just curious, but how much Historical Lore or events from the past will affect the Campaigns in the game, or will the Campaigns be semi-fictional, in nature?
The nature of the campaigns is not going to change from the original AoE1. This means that they will be semi-fictional, but based on historical events.
Personally i did not like the “fantasy” scenarios in the old campaigns ( eg I’ll be back, the Great Hunt ) and i would like the team to get rid of those and replace the with historically-inspired events/battles. Obviously not everything has to be historically accurate, just plausible. But this is just a matter of personal taste.
Bear in mind that gameplay should be always top priority when designing missions and campaigns. It’s nice and usually exciting to most people to replay history, but if you can end up with a campaign where every mission follows the same pattern, which is quite boring (compare city builder games). If for instance known Babylonian history lacked an event that would inspire a search and rescue mission (which The Great Hunt obviously is), you’d have to come up with a fictional one. Or maybe pretend that it’s some still unknown history. On the other hand, Xenophon’s March from Greek campaign is a historical event, and I remember it as one of my favourites.
But I see your point in I’ll Be Back, the backstory was quite silly. Seven Yellow Old Men, seriously Ensemble Studios? 
at least you knew from the very start to expect priests.