@SuperVegeta69 cool name.
Wouldn't say he was struggling, Kabuto was dominating them 3v1 and he'd never used the rinnegan before. Nagato would likely no / low diff any of them in a 1v1. Remember that Itachi was the only one with the battle IQ to counter Chibaku Tensei and none of them had the AP to counter it alone.
Minato Vs Nagato would be an epic fight as they're fairly well matched (Minato's battle IQ, fuinjutsu, and FTG will cause a lot of trouble for Nagato) but Nagato wins on hax. Chakra rods can disable Minato, rinnegan has some pretty broken abilities such as soul extraction (which should absolutely counter Edo)
Juubito not being able to phase is explained by manga events and the databooks entry for Kamui. We know it can be used with the Ten Tails since Madara did it. If the portal ability works the phasing ability will since it uses less chakra (chakra use is dependent on size of the object being transferred, phasing a portion of the body would cost less than an entire body). There's a single difference between the portal ability, offensive ability (Kakashi), and the defensive ability (phasing; Obito) that would make a difference and that's the fact that the defensive ability is an unconscious ability (automatic / passive) and the others are all conscious (active) abilities. The reason why this is important is that we saw how much trouble Obito had suppressing the Ten Tails, his unconscious mind was still suppressing it's will unlike Madara who didn't break a sweat.