Obviously if we don't resign Mo it changes the circumstances for Joba, but if Mo is back, Joba should be in the starting rotation. No doubt about it.
Joba has ace potential. You do not stick a guy with ace potential in the BP. You just don't. You can find good BP arms anywhere if you look hard enough. Look at Borowski. You don't find aces just anywhere. You can't pull them off the scrap heap. We have guys in the minors with potential in relief roles, and they should be given every chance to succeed before the Yankees decide to minimize Joba's value in the BP.
People draw comparisons to Papelbon, but the situation isn't the same. Papelbon has two plus pitches. Joba has three, and an average changeup. Just look at what he did to minor league hitters as a starter this year. He has great stamina. He can hit 97+ in the 7th inning. It would be like putting Verlander in the BP. Would he be awesome at it? Heck yeah! Would any one really consider doing it? No way.
Edit: I have also seen comparisons with Mariano. Those just don't make any sense because Mo flamed out as a starter. The BP suited him well in that case.