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[Trithemius]

Oddly enough, I dropped my focus from the navy entirely. Playing as Choshu, I focused on fortifying my assets, expand only slowly, one province at the time, and build up just enough forces to hold the province from invaders. I usually beat them to a bloody pulp when they assault my castle. Navy upkeep costs a lot of money, so I focused on ishin shishi and inciting rebellions in provinces behind enemy lines. Once my immediate neighbors find themselves with only a couple of provinces under their command, they lose the will to sail around my borders pretty fast.
When playing on harder difficulties, I found that the navy upkeep is better spent on the improvement of my infrastructure, and whereas I did in fact got bombarded few times, it was well worth the cost. Not to mention that once you've expanded you can go and build massive fleets within a blink of an eye and stomp everyone into the ground...Erm, water... Hmpf...

I neglected navy for a while (was going for British trading port so didn't make a lot of other naval centres) and I suffered a lot! I ended up with a lot of exposed coast and repair bills from enemy bombardment. It got particularly hairy at one point with many of my farms and towns being set afire by the angry guns of my (many) enemies - trust me to ignore navy while my enemies focus on it! They even pulled the rear-guard naval invasion trick once or twice themselves, the dastards!

[Voigtkampf]

It got particularly hairy at one point with many of my farms and towns being set afire by the angry guns of my (many) enemies - trust me to ignore navy while my enemies focus on it!

I think you did just right, and old Sun Tzu would have agreed. You don't attack your enemy where he is the strongest, but where he is the weakest. Take land troops, destroy their provinces and infrastructure, incite rebellions, bribe, sabotage, kill and maim. Lets see how many ships they can keep running from the income they pull out of smoldering ruins, harr harr!

They even pulled the rear-guard naval invasion trick once or twice themselves, the dastards!

And I like this, the AI is much better in this segment than all the other TW titles before.

[phred]

Playing as Choshu I built up my navy a little just to keep the coastline clear. I attacked a Nagaoka fleet that was blockading a trade partner and suddenly I was at war with Obama, Sendai and Nagaoka. oops.
They sent a steady stream of ships to harass me. Fortunately they sent ships one at a time and I was able to send out fleets of 3 or so ships to defeat them. Eventually I got wise and put a general on board. He leveled up very, very quickly.

To the OP: you should totally consider attacking fellow Imperials. In my current game Satsuma rampaged through Kyushu attacking everyone. Now they've declared war on Tosa and I imagine the Choshu (me) are next. I should have crushed them when they were smaller, but I've been a good ally. You should consider uniting Kyushu. fertile land, coal, copper are hard to resist.

[quadalpha]

The AI will nicely change their allegiance on the same turn they backstab you. You could call in all your allies, but it's better to hold off, since I find that if you defeat their invasion quickly, they'll accept peace right away and fall back into line without making peace with your allies.

[Azi Tohak]

Playing as Tosa with a bunch of allies (not just trading partners) around me, I simply hopped on fleets on the north and south coasts and took my fight to those Shogun-boot-lickers in person. It was great. I obtained military access from a little clan in the north and marched an army down from the province just below that hook, and then plopped a powerful army right on Edo's doorstep. No problem! But I was also playing a short campaign.