Well, for one, I can say this.
For some reason I cannot comprehend (I'm totally not a fan of PvP), most people exaggeratedly prefer PvP to PvE. The problem with this is that not only is Mabinogi not built for PvP, its PvP system is entirely broken. As in it favors archers to an unfairly strong degree. Granted, the balance has been threatened somewhat by charge and evasion, but any archer with half a brain can still thwart these, and they have some bad cooldowns anyway.
On top of this, losing in any GvE PvP means you get camped, and there is no way to escape other than persistance or leaving your computer until the other guy gets bored.
As for other things... there don't appear to be too many people playing with randoms anymore, and I can kind of feel the influence of that myself. "What will I get out of this? I'll probably be playing with some noob who does nothing but gamble rushes at his enemy."
The game is also heavy on some non-combat grinds as well. Especially if you're doing life skills. This generally tends to bring people down, and it's quite undesirable for most.
Granted, these are problems that have plagued Mabi before, so I don't know why that would contribute to people leaving now, but it should hopefully shed some insight.
^ Pretty much everything I hate most about Mabi.
Horrid PvP = no fun breaks between grind fests
Lifeskills...take forever to do