Kakuzu isn't stronger, Kisame's got much more impressive jutsu, larger scale, physically superior (movement speed might be equal but Kisame has much better reactions), a much better ultimate and quasi-ultimate jutsu in Shark Dance Water Dome and Daikodan.
Kisame's the full package whereas Kakuzu's ninjutsu combo's, the highlight of his AP, didn't catch a weakened Kakashi.
I lean towards Kisame being smarter too, but at the very least he's more analytical than Kakuzu. Kakuzu fell for Shikamaru's tricks, which is not really a downside to him, but he only recognized the problem after falling for it. And for Naruto he was completely fooled. Whereas Kisame deciphers Killer Bee's machinations and effectively counters 3 attacks at once in the span of a second.