But with an MMO theres no reason to play it if you can never be as good as the people that bot..
i don't see how that's an issue unless competition against players is an important part of the game in any way and isn't well thought out, in which case the game probably isn't that great even without bots
unless your motivation in the game is being the best or something
bots are only a problem if they actually affect the gameplay of others significantly. e.g. breaking the economy of a game or just general exploits of broken systems
in a game like OP is describing, this may not be an issue. however, paper mario is singleplayer; the transition to a multiplayer environment isn't so smooth, so it'd be interesting to see how that could be accomplished.
edit2:
do keep in mind, everything bots do
can be theoretically achieved by humans. bots are used when this kind of task is monotonous, boring, or if the player knows they can consistently seek rewards. AKA grinding. the argument that making a game around grinding curbs bots is ridiculous because bots generally are made and used so that the player doesn't have to grind actively
and if a game is designed so that a player of greater rank/skill level can easily ruin the game for others, the design is flawed. again, this could be achieved with or without a bot theoretically, as bots don't hack the game in any way (unless minor 'hacking' is required for the bot to function).