So something odd that happens in Hanzo's SW 3 story (and I think Ina's or someone else's) is that Ieyasu wins the battle of Komaki-Nagakute and allows Hideyoshi to join him in his conquest (historically, it was the other way around). Just two stages later, Ieyasu is working for Hideyoshi. I know it's likely an oversight and they'd have to make another version of the stage just for this situation but still.
If you actually look at it they never truly let Ieyasu "win", just avoid conquest, so it's more like "win the battle, lose the war" kind of case.
Any reason why the games ignore the Ashikaga Shogunate's collapse, I mean, that part of history is what lead to the Warring States Period, didn't it?
With the addition of Hisahide in SW 4 it looks like there may be some focus given to it.