tactics, awareness, strategy. Whille both possess power, Kabuto isnt one to jump into any fight without thinking and analyzing the situation, which is his position he could be the 10x over. If I'm not including Edu, i wont include Tobi's beast. As a result, Tobi remains a confident idiot (IMO) he wouldnt expect Kabuto to control any non-living object and would try to simply espace and #boom get caught in genjutsu as Sasuke, Itachi and Nagato (pein) did. Naruto as is remains to speed demon with limited resources, which Kabuto would only have to do is defend (as Oro did majority of his fights).
we could go deep into this, but this is my brief prediction.