As stated before, if everything goes well with this project, come time for the games release, we hope that the player base will be massive and global, thus making the .02% fine and dandy. Ya feel me?

It is called an MMORPG. What other games are there that are also MMORPGs? World of Warcraft. So one can only assume that there will be missions, and that there will be NPCs whom give out missions. Although, I would /love/ to see the Kage or high ranking Shinobi/people to give missions as well, it'd really add to the diversity and variety of missions and mission difficulty.

There will be an academy test in the game for which you have to pass to reach genin rank. There will be a library where you can learn about the Shinobi Life Online Universe for that test.

Calling out jutsu names is a great suggestion, although not something you'll see anytime soon.

Have you come to a conclusion on how you're going to insert these exams, and by that I mean, have you figured out what they are going to be like and how they are going to work? Come to think of it, in order to come up with an exam that fits all together, you have a large amount of stuff done before you can think of that, but know that I am not you so I don't know everything you've done/are planning with it!

I kinda strayed from my question-- What are the exams going to be like? Will there be the same amount of exams as there were in the Naruto series and will the exams follow closely to the one in Naruto?

Destroy-able environment has already been discussed by Vreg and I, and apparently it's really hard to have it implemented and make it look great, make it re generate etc. So unfortunately it's very unlikely to have that.

I believe this, but by the chance you guys do manage to implement the whole 'destroy-able environment' and it being able to 're-generate', it should only be in places far away from major villages.
To clarify/add onto my point: Let's say it's years and the game is flourishing, it's a massive game with a massive player-base. There is an extremely strong (If possible, but it's just for the immersion) group of shinobi, like the Akatsuki ! They decide to get together and attack a major village to free someone from life imprisonment (If that's changed I don't know, but off the top of my head, how would that be done, the whole "Breaking someone out" thing? anyways). The group, we will call them Taka (another reference!). So Taka invades said village and throws paper bombs attached to kunai everywhere, boom boom boom explosions. This shouldn't destroy anything like buildings or roads because that would be too much of a hassle to fix, I am sure of it. I am also positive, possibly wrong, that it would strain the server or the game if there were bricks and buildings flying everywhere because let's face it, people would randomly throw paper bomb kunai everywhere because people are cruel. Back to my point, nothing in the village is destroyed, or at least nothing important like buildings or streets, etc. Taka gets their member and escapes, but oh no! they are being pursued.  After quite some time now, Taka decide they are far enough from the village to turn on their enemies, and a fight ensues. Maybe some more kunai paper bombs are thrown or some jutsu occurs and uproots/destroys some surrounding trees. I feel as though, being far away from a main village, those trees should be visibly gone, destroyed, maybe some wood on the ground, I don't know. Same goes with small towns or singled out houses or stuff.

TL;DR- Main villages shouldn't be destroyed, but far away in forests or small towns, singled out buildings or maybe another persons clans stronghold, would be destroyed if the jutsu is strong enough or paper bombs are placed. It'd add to the immersion of the Ninja world/realism of the game. This is only assuming you guys can and will add the destroy able environment. And if you guys do, and you make it regenerate able, then the rate/length of time it takes to regenerate should be one high amount.

Need anything clarified in my sloppy text or have any questions feel free to ask!