That smartass tl;dr comment almost made me not read this wall of text but my curiosity gave in. I get that you were kidding and I didn't get offended in any way but it just shows lack of consideration from your part mate and imo kinda gives away your lack of maturity...
Buildings: From what I've heard, the community will be able to design some buildings (not sure if only on the designing stage or also when the game supposedly comes out), if there's a management side to controlling a village then I think we could start with a pretty basic village like the one we have now and then build these kinda stuff as the village grows. Not sure this is the case though but imo that'd be pretty cool.
Although yeah buildings like library and prison should be standard. I think we'll have restaurants to start with as well.
Levelling: Levels are by far not the only way to engage someone. The ELO rank would probably suffice to keep people motivated to play. There's a special sense of freedom in being able to do every jutsu if your chakra enables you, you'll try and find new jutsus, learn them and beating someone by mere skill, jutsu knowledge and physical development (aka hp and stamina). That imo is much more fulfilling than getting squashed by high lvl characters who are invincible for lower level players. Anyone could beat everyone with actual game skill instead of with time spent playing the game.
Ofc the more you'd train a jutsu the easier and better it'd get in-game.
As for the issues
@Manuster shared, there's a simple solution to all that: Experience is dealt based on damage given+hp recovered. There could be some more variations into this such as points for trapping an enemy or luring towards a trap and stuff like that but the original formula would already cover most damage dealer and medic shinobis.
But overall I'm against levels in this game.
Rankings: Well I'm not sure I completely understand your aversion to ELO ranking but I kinda exposed my point already. With the adjustments I proposed it should prove effective for all kind of shinobi. No leveling up, just experience gathering with some weapons/jutsus to make them more effective and ELO system based partly on this experience, missions performed and fights won.
@Vreg seems to be a reasonable person so I think he will be able to balance out fun and logic in this ranking system, my way is just one way of doing that imo.
As for the
exams you all don't seem to be taking into account the kind of people that'll be playing this game... To make the game interesting for everyone they should indeed stay as academy students for only a short period of time (say 10h in-game) and make an exam that actually requires some amount of training, otherwise people could just leave their computer on for 10h. Say consecutively performing a set number of jutsus from a big pool of basic jutsus so that they have to study several of them. It'd also serve the purpose of a tutorial but it'd be masked as an exam.
After that there'll still be lots of people that are definitely not team players and will want to screw other people on the exams just for the "fun" of it. Those people should stay gennin or academy students for life imo until they learn to work in a team so I agree with having a team based chunnin exam
provided these idiots are not accepted. So we'll need to wear them out (they get bored easily fortunately), 3 weeks mandatory as a gennin seems reasonable but also send them on missions that rely on teamwork to pass or in which they have to interact with someone (persuade someone to do something for instance). They'd have to go on a required number of these missions before taking the chunnin exam.
However when designing this stage Vreg wil have to keep in mind the different timezones and schedules of people, it wouldn't be a very interesting experience to be assigned to a team and barely be able to stay online all 4 because of personal/professional reasons. Considering most of the fan base for this game are probably teenagers and young adults I don't see lots of people with the schedule versatility this game might require...
Regardless, apart from maybe these (let's call them) "traditional rules", additional rules and exam format should be up to the kage to decide honestly.
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