What I mean by stating that it's a part of the game is that that is how the game was built, structured and intended to be played initially. I never said it was going to be like that forever, in fact I even mentioned how jobs are taking that away for party play. If you play a class, you're going to want to cross class. If you play a job you'll probably be okay with just the job. Keep in mind though the distinct possibility (as mentioned in the famitsu translation) of cross class jobs too. There's a reason you can level all classes on one character.

For now those who put in the extra time and effort to have those cross class abilities are better for it. They should and do have a distinct advantage.