The alicesoft Wikia tells you pretty much everything. However, Mouri has taken over Tanegashima and/or Akashi on my second or third playthrough, so I think I'm calling shenanigans on that.
I've done the True and Ran route and am working in the Isoroku route as I speak. I find that I'm using different characters every time.
First playthrough: I never used call for reinforcements as my cost was always maxed. Little did I know then that I should've just fired some newbies and made space for the awesome that is MORE HSCENES AND EPIC COMMANDERS! I also attacked Takeda first out of the big 3 Northern Japanese families (after getting through Hara, Ashikaga, Iga, Tokugawa, Iwagawa, and Asai-Asakura) as it seemed like the most heroic thing to do. This was a fairly bad idea, especially when Houjou decided to attack me. (WTF?!#?!#?) However, this is the only way to get some nice tebasaki (cavalry) units. I didn't even get the Takeda commanders (except Sanada Tourin who you automatically get), because soon after the Demon Army stomped around on everyone else.
As such, I had fairly few "special" characters (ones who you can talk to to increase affection as opposed to those you can't). I used Rance, Ranmaru, Shibata Katsuie, Suzume, Isoroku, and generally Sanada Tourin. For the final battle where you can't use Rance, I used Ranmaru, Shibata Katsuie, Tanegashima (the lego-man), Suzume, some random Cavalry dude who was fairly strong (cavalry fkin OWN), and Sanada Tourin (Battle rating down 2 WHAT?!@?!)
I also managed to finish the Orochi dungeon in this one without the Emperor Sword, which I didn't even find until my second playthrough.
Second playthrough: Going for the Ran route means NO DEMON ARMY. As such, while you may have plenty of time to recruit commanders (see: all game), you may very well be attacked by 3-4 powerful nations at once! I got attacked by Shimazu (who owned Mouri who took over Tanegashima) who now had 4 Shimazu bros, Agireda, Mouri Matanari, the 3 mouri sisters, and Tanegashima and Yuzuhara Yuzumi. On the northern side, Takeda and Uesugi were attacking me at the same time as well.
I managed to get Akashi because I wanted to see the storyline, and I went after Houjou quickly to get the Ran route.
However, I saw the power of "call for reinforcements" from the Wikia, and decided to call in Rizna (Zeth), Kentou Kanami, Maria, her subordinate Kasumi (or something like that, I fired her immediately), and Leila the Knight (All of these from Leazus).
There's no final battle for this one, just a final dungeon full of commander battles, and really all that shines here is what level your units are. Besides, you use everyone in your party. However, Kenshin didn't really stand out in commander battles for me. Mainly, my good units were Rance, Ranmaru, Shibata again, Maria, Sanada Tourin, Shimazu Toshihisa (yes you can get the Shimazu bros in this route), Ran (You thought Natori's miko storm was good? Advanced Shikigami is EPIC with 8-9 intelligence), and Leila. Really though, their dungeon fighting strength was more important.
Third playthrough: I've started to go through everything now that I have a lot of bonus points (55) to deal with. Firstly, the best bonus character is by far this epic monk that goes by the name of Makutsudou. With 9/8/5/4 stats out of the beginning, monk charge plus, and convert action 2 as well as youkai ward, this guy helps you crush the early two houses extremely quickly. Add a popularity staff to him (from your bonuses) and lol.
Then, I reinforced from Zeth first to get Rizna, Uruza, and Magic. Check this combo. Kenshin + Uruza + a convert action monk (Aburako Dousan or Makutsudou). Kenshin -1 action. Uruza accurate shots -1 action. Convert action on Uruza. Accurate shots again -1 action. That's -3 actions! Pump speed into uruza and your convert action monk and you should be able to do it before any of your foes spend two action points.
This is the first playthrough I used whirlwind shot on Isoroku, and it's a much better decision that Foot Soldier Snipe which I was using before. The one-shot kills are actually fairly often once you have many troops. I also got Yuzuhara Yuzumi relaly quickly, so I'm trying Working Bee on her, despite the original handicap of killing half your original troops (+2 actions, and aim and shoot only costs 1, and it has a chance to instant kill!)
Rance is actually looking pretty shabby compared to my other units. I'm looking at Rizna, Uruza, Isoroku or Magic, and in the front we have Kenshin, Shibata Katsuie (healing his injuries makes him a great tank), and Makutsudou.
