There isn't one. You can farm the rare ninjas just as you do the other ninjas. The ones from the packs tend to have better abilities and make more interesting teams. Eventually the shops will contain all kinds of rare ninja to farm so you can have your 5-star Itachi or 5-star Asuma Wind Blade or 5-star Gakido.
But as far as power differences, just comparing my 3-star Neji to 3-star Kisame shows that Neji is basically superior except for a slight Ninjutsu imbalance in Kisame's favor. Except Neji doesn't care about Ninjutsu, only his chase uses it and it also uses Taijutsu. He's not suffering from the lack of it. Kisame looks weak by comparison.
Yet Kisame's abilities are what make him potentially better than Neji. His healing, autoattack acupuncture, increased attack rates, an offensive AOE jutsu, all things you might favor more than Neji's simple setup. Neji is an actual tank because of his rotation while Kisame is squishy but 5-star Kisame can be less squishy and he does heal for a percentage of total health.
Even Tendo Pain isn't very scary when stats are looked at. I regularly destroy him and the other pains with Taijutsu teams. But if you're running Ninjutsu teams he can be a nightmare. The utility of rare ninjas make them peculiar and more able to synergize power combos which makes up for their lack of stats next to 5-star ninjas. A 3-star Tendo Pain will still be in ninja wars because his ability is just that good.