I think what this thread really comes down to a select few people who like to either hide in a corner and rp all game or others who like David vs. Goliath stories and think David should win everytime. If Goliath wins once they cry "omg wtf this game's ai is overpowered and favors blobbing!" But if Paradox listens and breaks down the ai then another group or even maybe the same group will come in and cry "omg wtf this game's ai is too easy! It sucks! I started as a one province clan and chewed through a 36 province clan in 3 years!" Also I find this game pretty deep for what it's focus is. Sure the combat system is on the shallower side of Paradox titles, and the economic system is non-existant but the relationships, clans, and world are surprisingly deep.
This game comes down to 3 questions for a player: Do you want to win? If yes then you SHOULD play a moderate-to-large sized clan as that would be the most tactically sound choice. You should not your first game (when you don't even know how to play yet) play the tiniest clans on the map and expect to be the top dog in 10, 25, or even 50 years.
Which brings around question 2: Don't care about winning and just want to have a good experience, and just live life as a sengoku era clan? Then your strategy shouldn't be to make the big clans angry at you. Sure there is no non-aggression pacts, no alliances. But you don't need them to keep a big clan off your back. Build the crap outta your castle, and use hostages+gifts+master of ceremonies+a good leader diplomacy skill to keep the biggies off your back. Then if your game comes down to the battle of the blobs, then maybe you need to work with ninjas, the remaining small clans, and factions within the big clans to bring about civil wars in the big clans and bring the game back to square one. Just where you like it.
Finally question 3: Don't care about winning, but don't care about rping, you just want to have an enjoyable game, maybe even a laid back game? Then you should pick whatever clan you want, and stay on top of Japanese Politics. When clans get too big, take action against them before they get to you. Whether that action is cementing good relations, or plotting insurrections. Heck you can even Join em if it comes down to it. (can't beat em? Join em)
If all else fails. Mod it. Modding Paradox games is easy and popular. Most PC games are just the building blocks of the perfect gaming experience for you. Design it yourself, or beg someone else to. I'm sure people will be modding scenarios where no clan owns more then 1 province, and I'm sure people will be modding scenarios where clans only have 50 provinces or more.