This is the reason why I am not a big fan of Tactician, Conqueror, Cavalry and Naval. Since they are almost indistinguishable from Lion, Spider, Unicorn and Mantis.
Actually what I would find interesting would be if the Clan alignment would give you a clan specific effect... Tactician for Lions for example, Kensai for Dragons, Duellist for Crane.
Since the clan alignment is now a mon and a frame this would save much space on the cards...
If they keep strongholds, I doubt if there will be separate affiliation cards.
I wouldn't want built in clan rulebook abilities, but those seem like they'd be fine (if very basic) stronghold (or affiliation) abilities, if such things exist in the new game. They'd need some balancing, though. I mean, Naval seems like kind of weak sauce vs. Tac or Cav, generally speaking.
A good weapon or follower on a naval personality can go a long way to making meaningful impact when attacking a province like a Bishamon's Bow . Its also good because its a baked-in version of the Sneak Attack strategy which means you have the first battle action with a Naval's unit when attacking.
However its more like comparing a Crane to a Scorpion and vice versa. Sure they both have their practical purposes, but they function differently from one another.