Mind the seasons
Each turn in Fall of the Samurai reflects just a few weeks of time. In previous Total War games, clicking the End Turn button could move the game ahead an entire season. This has some knock on effects that you'll want to keep in mind as you plan your conquest of Japan.
Winters last a lot longer. If you leave armies out in the field during the winter months, a number of soldiers each turn will freeze to death or desert. As it can take many turns to train replacements, you'll want to keep these casualties to a minimum by planning around the winter months. When you plot an army's route on the campaign map, you'll be able to tell how long it'll take them to reach their target from the number of times the arrow changes colour along the journey. Making a note of this will help you avoid stranding your armies in the cold.
That means the winter months are good for up your forces and planning your attack. When the snows thaw, start the war.
Manage the pace of change
Moving down the new tech tree in Fall of the Samurai can be a dangerous business. You gain new advances by increasing your faction's overall modernisation score. You do this by building modern buildings, researching certain civic techs and training advanced troops. Their are several tiers of modernisation to unlock, and each time you cross into a new tier, the chances of a samurai rebellion increase.
As you start to head into that final tier it's a good idea to pull some troops off the front lines to garrison some of your central towns. When the samurai rebel, they really go for it. Large armies of them will pop up in the middle of the countryside in your weakest lands. They'll make a beeline for the city of that province, trashing your mines, farms and taverns as they go. Build structures that increase repression to stop this from happening, and keep your forts well stocked with troops. Their mere presence will discourage disgruntled warriors from turning their blades against you.
Be aggressive with your allies
Just because you're allied with a faction doesn't mean you're not in competition with them. There are a lot of factions fighting over a limited amount of territory in Fall of the Samurai and you'll have to be boisterous if you want to take more cities than your nearby friends. Securing lots of territory early on can solve problems later in the campaign when the only territory you can feasibly take belongs to an ally.
Betraying a faction you have a long term relationship with will have a negative effect on all of your negotiations. Word travels quickly, and the other faction leaders will quickly get wind of your backstabbing behaviour and trust you less as a result. Damaged relationships have a direct impact on the amount of profit you make from trade, which makes all-out war with friends a bad option.
There are sneakier alternatives, though. When the campaign starts, there's a rush to conquer the many tiny factions scattered across Japan. If you don't take their territory, your allies will. I often found myself racing allied armies to undefended enemy cities. In these situations I would employ Shinobi agents to sabotage allied armies. This would freeze them on the campaign map and give my army the chance to occupy the province that should have rightfully been theirs.
If your Shinobi is good he'll complete the mission and leave no trace. In that case, sabotage isn't an act of war. Your ally might suspect your involvement in their army's difficulty but they'll never be able to prove it. The perfect crime.
Turn the enemy
There are several new agent types to scheme with in Fall of the Samurai. Used them well and you can destabilise enemy provinces and even turn enemy troops to your cause. Imperial factions can recruit Ishin Shishi agents, Shogun players can recruit Shinsegumi. They play very similar roles on the campaign map. They're good agent hunters, can repress rebellions, inspire friendly troops or waltz up to enemy generals and talk them into joining your cause.
It's worth sending one or two agents wandering through the wilderness, converting small enemy forces whenever he can. These turncoats can hang around behind enemy lines, sabotaging resource points and throwing themselves suicidally in front of large enemy forces to slow their progress. Cruel, but effective.
It's worth remembering that some targets are much more precious than others. When you're harassing enemy provinces, you'll want to burn trade ports and advanced resource gathering structures to the ground. Above all, you'll want to target railway stations.