And those are trivial to go around. But, phone verification is much harder to get around. Maplestory 2 Mesos may be as simple as replying to a text message, or getting a telephone call and moving through an automatic method (eg. "Punch on your pic to verify that you are the one who made this account.") , so that no one is excluded if they don't have a phone.
Then, NexonNA just needs to need this on all newly created reports. They also need to connect each phone number to a particular account. If this account receives a ban, so does the phone number. This way, once a bot account is banned, it is going to require a new phone number to generate a brand new account.
Phone numbers, while plentiful, are far far less plentiful than ip addresses are. This puts a massive barrier which only gets more successful over time (as an increasing number of telephone numbers are blocked) against bot accounts. However, it doesn't hamper legitimate gamers at all (because, frankly, in case you've got a computer that can run MS you've got access to a phone of some kind).
I understand that there are a number of disadvantages, but I do not believe they're large enough to justify not implementing this system. The biggest drawback I can see is that a bot/meso farmer uses your phone number and has it banned until you try to produce your account.
In that scenario, there might be a rather intensive approach to clear a phone number (it might have to be intensive to be an effective ban). Either that or you are out of luck, but the odds of that happening anyway are slim to none to begin with.