The only two baseline skills I see needing an update are Seigan and Ageha.

Ageha primarily because all the execution abilities are boring AF.

Seigan because it's a hoop to jump through while only being slightly stronger than Shinten while occupying the same purpose (OGCD Kenki attack).

Actually, throw in Third Eye there as well.

Third Eye; Seriously should block more damage as a small window single attack damage reduction. 20% isn't unreasonable here.
Seigan: Move into a Reactive Weaponskill around 280 Potency but generates 15 Kenki. One use per Third Eye. Enough to be worthwhile to use but not to the point where the Samurai would want to risk death without having healers who encourage it.
Ageha: Lower Ageha's Cooldown. Remove the Kenki on use, give it a Kenki cost. Increase the potency as Enemy health lowers (Something like 200-500). Killing blows refunds the Kenki twice over.