Can anyone explain the Faction War in detail?

You spend your score from each match to either defend or attack an area. Every two weeks there will be spoils of war to the faction with most land. You can spend your assets on any area you want, not just the place you fought.

What happens when a Faction loses their stronghold? All of their territory? Can players from that Faction still participate and take back territory? Or do you effectively stop contributing to the meta game until the next round or season if your Faction gets knocked out? No idea about this, nothing has been said that I know of

Do we get different maps depending on where you're fighting on the world map? This question is a bit confusing, so... I'll answer two ways. I'm not sure if the map rotation is different based on where the faction war is (I'd assume not, all maps always available). Now other aspects of the maps do change and I'm not sure WHEN but apparently they do - I haven't paid enough attention to know. When a knight/Viking/samurai map (citadel/river fort/sanctuary bridge respectively) is taken over by another faction in the war, then decorations such as flags/emblems are replaced by the faction that took over. Without knowing where these maps lay on the faction war map it is kind of hard to know when these changes will take place.

What are War Assets? Is it better to save them and try to "swing" a zone before the next round? Should I be focusing on one zone? Or spread it out? Do they expire at all? War assets are like a reward for finishing a match, the better (kind of, because also the longer it seems) you do in a match (again - for some reason going 3-0 in a duel will give fewer assets than 3-2) the more you get. You are unable to save them and if you don't place them before leaving a game lobby or starting the next match they are deployed evenly between all the territories your faction is defending/attacking. Usually it is best to manually deploy all of your assets in a territory where the percentages are close (48-50%) as opposed to one where you are winning by 10%. Up to you to decide if you can impact a zone where you're losing by 10%.

Why do some zones have only knights and samurai fighting for control (49% 51% split) and others have all 3 with something like (49% 50% 1%)? Should I ignore these zones where my team is the 1%? Would I be able to make any difference at all? You can only fight along your front, so it depends which territories your territories are touching. You probably won't be able to win that 1% but you can try.

Do players who only play one mode cripple their team as far as the meta game goes? I've seen the game modes rotate around the map a good deal. If I only play Brawl and it's currently being played in Viking territory but my Knight brethren are being smashed back home in Dominion, should I switch modes to help? Yes, but no, but meta yes (kind of). There is a 20% bonus for using assets on the front you got them (where the game mode is) Now you can probably still get more points in a dominion/elimination match than in a duel/brawl with the 20% bonus, just check it out by trying a couple matches and see what you can get.

What do you get if your Faction wins the season other than bragging rights? Just some flair?In the open beta, just emblems I believe. In the actual game you get gear and some other things (I can't really remember but it is mentioned in the faction war tutorial video) I recommend watching that.

Do players who join/switch Factions after a season ends get those rewards? This is touched on in that same video, no rewards for the season you switch in.

What is the plan for events? Time sensitive one offs like Hitman Elusive Targets? Or can we go back and play old events? Are there going to be rewards for events? There is an event to start in about 5 hours, you will see, don't know much more than that.

I know the game hasn't even come out yet so this type of meta game strategy hasn't been solidified but I don't like running around like a headless chicken while these weebs are taking the Holy Land! All joking aside this game is so much fun. I have hardly had any issues with the game server-wise so far. Fingers crossed for a steady launch so this game gets the hype I think it deserves.

What happens when a Faction loses their stronghold? All of their territory?

No idea since it hasn't happened. I doubt they'd lock players out of the faction war, they'd just likely have to git gud and take it all back.

Do we get different maps depending on where you're fighting on the world map?

Cosmetic differences, yeah..

What are War Assets?

Depending on your personal performance in every match, you'll get some war assets. When you choose to deploy them, you shove your numbers into a territory that gets added with your faction total. The faction with the largest number claims that territory at the end of each turn. If you don't choose to deploy war assets, the game will instead spread out your assets evenly across every battlefront your faction's fighting in. This can lead to wasted resources in areas you know you've won/lost, it's better to focus on contested areas.

Why do some zones have only knights and samurai fighting for control (49% 51% split) and others have all 3 with something like (49% 50% 1%)?

Every game mode needs to have at least one contested area where a faction can place their war assets into it.

[...] should I switch modes to help?

When you go to deploy war assets, you can back out a bit and place them into another game mode's areas. You'll lose the 20% bonus of placing in an area matching the game mode you played, but it can be done.

What do you get if your Faction wins the season other than bragging rights? Just some flair?

So far, the rewards are emblem pieces and borders. Ubisoft's video about the Faction War shows that eventually gear (armour/weapon parts) can be awarded, and implies helmet ornaments can be too.