Although the game is overall very fun, certain aspects can be annoying.
However, certain aspects of it are unappealing. For example, if you aren't a big saver, then this game will KILL you. Dying in battle moves you back to the point you last saved. If you accidentally slip up and realize you forgot to save a while back, you have to work your way back.
This game is also filled with unappealing challenges that are all pretty much the same. "Track something down and kill it" being the primary challenge. In most parts of the game, you're saddled with finding something specific and killing viruses. Although this does sound appealing, the 7th time you do it, it's less fun.
This game, at times, is also filled with repetitive dialog. For example, in one of the levels of the game, you have to go through a mission to unlock a door. Geo (the main character) constantly says to find a Wave Hole. Four times. This happens constantly throughout the game.
All in all, if you're looking for something that'll kill boredom, go ahead and buy this game.
Oh yes, and the ability to receive uber-powerful cards through codes ruins some of the battle system. *cough*