I cant really say Mana is hotter than Motoko... but I will say this, she is very hot, I'd consider them on different plateaus.
Mana carries her self more stoically than Motoko, is in even more control of her emotions yet does not let it afect her femininity, she has that nice 'cafÚ con leche' tan going for her, marvellous sharpshooter skills and does know her way around a shinto shrine.
Motoko's strenght comes from the Shinmeiryuu... and as I've come to interpret it, the strenght of one's heart, and the desire to protect others (especially loved ones). While she is beautiful, she has much to learn about life (tho in time we notice her growth).
Kanako's beauty lies in the mystery about her, strong and sometimes vicious, she does let herself be beautiful to (try to) pull her beloved to her.