WHY THE HELL WOULD HE TELEPORT BACK ALREADY!

They basically had Obito beat! They'd awesomely figured out how to get around his invulnerability. All Kakashi had to do was stay there and use a REAL attack instead of some stupid punches when Obito phased through an attack.

Instead, he comes back. It doesn't seem likely that Obito will suck him up again, so now, he's basically invincible again.
Kakashi can still teleport Naruto's attacks so Obito cant pass through them. I agree it is much less effective but they still have means to deal damage. Besides what happened to all the other people he has sucked up? Who knows what happens if you are sucked up for too long. Seem to be no remnants of some powerful Shinobi.