Mind if a noob might share his opinion?
I think an MMO type game with stages is a bit unorthodox, but it can work if it's handled properly. The first idea i had would be a simple one, where basically (like SM64) theres the main lobby that goes into all the stages. This would be the main place where people would interact, party up, etc.
Then, also akin to SM64, you would only be able to go into the starting stage at first. You could conquer any of the missions either by yourself or with friends. After completing the mission, you would get 1 point (i don't really know what the points would be called since this RPG seems to still lack a theme), and enough points would let you move onto the next world. There would also be many missions per world, maybe just 8 or 10, to stave off any repetitive nature.
The catch to this would be that if you complete it with friends (parties could only consist of 4 people max) then the point you receive for the level gets cut in however many people you had helping you. For example, i go into the first stage, i get 1 person to help me. We each get .5 points each. If i had 3 people helping me (making a total of 4), then each player would get .25 points from it.
There would also be boss stages in each world, however there would also be some larger fights in between the worlds, in which you're forced to work in a party of at least 2 people in order to fight. Boss fights would give some other reward than points (possibly gold? I'm not sure)
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Well, thats the first idea. I don't know whether the one i'm about to list now is more complex or not, but...
You could also make the game have a PVP theme, where each stage you go into is a race to complete it fastest and best. It pits you against 5-7 other players in an all out race to finish, and or accumulate the most gold from defeating monsters, the stage. The point system would work similarly here to my last idea, except this time parties would only be allowed during the large boss fights i talked about earlier. You'd be on your own competing against others with this idea.
Whoever finished the best out of the stage, gets the full point. The others who finish behind get lower than that (for example, second place gets .80 points, 3rd place gets .60 points, 4th gets .40 points, and 5th only gets .20 points)
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theres a few problems i'm already foreseeing with my ideas. The first is that, for the second one, this game would have to be really popular for it to work well. Also, i'm not seeing much replay value here, because once you get to the end, i'm not really sure how to freshen it up.
The second problem, is that this seems really complicated. Working with something like RPGmaker XP, coding this would be extremely EXTREMELY nausceously difficult, especially with all the interaction between characters involved in this.
But hey, you don't have to take my whole idea, or any of it. Just thought that i'd throw my 2 cents out there as to what i thought would be pretty cool.
(Oh, and also, i really like the idea of each stage being a tribute to a different SNES RPG. Like, one stage could be chrono trigger, another stage could be Secret Of Mana, and another one could be FFIV (they wouldn't have to play like them, that would be asking WAY too much). Each one could change how many you can have in your party, for example for the Chrono Trigger and Secret Of Mana stages, you can only have 3 to a party, but in FFIV, you can have 5.)