The chakra conversion probably makes it easier for the Shinobi Alliance people to handle/maintain. I'm not sure if the Kyuubi's chakra is still harmful to anyone besides a qualified Senju/Uzumaki style Jinchuuriki; Minato described it as "heavy", and obviously we remember Sakura's injured arm that remained "poisoned" by the Kyuubi chakra, leading Yamato to marvel that Naruto could withstand it.
Kurama is no longer evil, and it wouldn't make sense for his chakra to be harmful, but perhaps Bijuu chakra is inherently difficult to withstand for the average human. It seemed like Kurama used his own chakra to revive Kakashi, but maybe even then he went through the conversion process to provide Kakashi with additional "Naruto brand" chakra.
It is somewhat unique that, when Naruto wields the Kyuubi chakra, it gains interesting properties like Mokuton-enhancing Life Force (which seems to point towards some sort of Senju/Uzumaki qualities at work, somehow). I'm waiting for the fight to progress to the stage where Naruto's "Nine Names" / Sage Mode come into play; I'm guessing some way or another, his "Rikudou Reincarnation" status will be explained, and perhaps the unique nature of Naruto's chakra and Jinchuuriki transformations will be explained as well.
It definitely is fishy that Naruto possesses so many unique powers that Bee does not, such as Chakra Modes, evil-sensing, and Life Force. The Eight Tails doesn't seem to grant any unique traits, aside from possibly the whole ink-spitting thing.
I also wonder if perhaps the ability to fully convert the Kyuubi Chakra into Naruto Chakra will be what finally allows the combined Kyuubi/Sage Mode most fans have been anticipating. I could understand Naruto being unable to manage both modes if he must shove his own chakra aside to enter Bijuu Mode, or must balance mental/physical/natural energies with Bijuu chakra; however, if he is indeed able to skip the balancing of Bijuu chakra while wielding the full chakra capacity of the Kyuubi (in Bijuu Mode, no less), then this could be the final step.
At the very least, Sage Mode needs to have some importance! Sure, it allows Naruto to sense the immeasurable capacity of the Juubi's Natural Energy better than others... but if Naruto could magnify his Natural Energy-gathering capacity to Bijuu levels, maybe he could even make a dent in the Juubi's own chakra reserves, thus helping to balance the scales.
I'm not saying the Juubi will be defeated with brute force (or even can be), but it'd be cool to see Kyuubi/Sage Mode make a relevant contribution to the fight.