I wouldn't mind the rise of the Mantis in the new storyline nor their existence as a faction in the LCG. For most of the other factions, though, I think they should just refrain. I got into this game with a Naga deck but once I knew more about the lore of L5R the less it seems they should be an active faction, unless they are rewriting how they exist in the world. (If they're a living empire next to the Empire or some such then sure, make them a faction)
Otherwise, leave Naga, ratlings, monks, Ninja (with a capital N), minor clans, etc. as "splashable" characters available to any clan just like Imperials always have been. I think its just cleaner and doesn't distract from the root of the Great Clan conflicts. Again, if Mantis eventually rise as a power (whether as a clan or as Yoritomo's Alliance, or even the Three-Man alliance without the Mantis) then sure, make them a consistent faction for the game from there on out. But nothing that's going to come and go. That's just gimmicky.