I hate to say it but what make an MMORPG big ? You need to go to the roots. High immersive  levels of customization. Everybody in the world wants to be unique so let them. Give them more options on customizing there ninja all the way down to color of nails. Let players choose what village they are from then base there jitsus from there. You can have skill trees for the three types of Jitsu's . One being TaiJutsu , Ninjusu and last being genjusu. Make sure you be creative and create your own jitsus for the characters. Base all seperate skill trees based on village this will truly make players unique. Now you have to think about other MMO's there are healers , tanks , utility/support, DPS. For example I see a Gara like character being a tank and I see TenTen being a utility. You can even have summoning skill trees or even a separate class. Make sure its based on village as well.

Now for gameplay all MMO succes is based on loot and items. Even in the universe of naruto you can still wear cool clothes and have weapons just take some creativity. Maybe ninja scrolls to learn new abilities .

Now lets talk about stats and currency ..... needs to have stats enough said..... im talking this game needs to surpass runescape.
In the show of Naruto they emphasize many things that i also believe can be transformed into stats.
Cooking- Ramen for example
Crafting - Always repairing buildings
Herbs- For potions and healing / Boost
Bounty- Capturing rouge ninja
ECT
Ill have more ideas if people liked the ones i have came up with Thank you for your time