Bayonets for FoTS: http://www.twcenter.net/forums/showthread.php?t=538081
Most of the troops in this period were Samurai that had sided with one faction or another and adopted modern weaponry. Essentially, any "quality" infantry formation you'll recruit will probably be samurai based, just using rifles, rather than traditional armour. Hence the swords as the melee weapons for most, if not all, of the troops.
Conscript armies didn't really become common until after the Boshin War; the Satsuma rebellion was more of the modern conscript force vs Samurai, and even then almost the entire office corps of the Japanese military until WW1 were former samurai. Equipment doesn't make a samurai who he is, it is the mentality, the philosophy.
In more gameplay terms, from what they've said, traditional unit types become less effective over time (lower morale perhaps) or have limited recruitment as you advance up the tech trees to reflect the focus on modern arms, rather than traditonal ones. In fact, if I recall a posted screenshot, the very first "starter" techs are Shih and Epic Architecture, the last techs from Shogun 2. If you want to go really traditional, all you have to do is not research anything, which has its advantages due to not getting a public order penalty for modernizing.
Were I to take a guess, the Shogunate's troops will remain more "samurai-esque," with the focus on melee skills or cavalry as they modernize, or perhaps overall better martial stats at the offset of higher costs, to represent Samurai dedication to their chosen art, but also the long training time involved, while the Imperials focus more on conscripts and modern military professionals, so more "shooty" and less expensive, but that's only a guess. It's hard to say what the Shogunate would have done if it survived, because, after all, it didn't.
Therefore, I conclude, that Valve should announce Half Life 2 Episode 3.