There actually isn't much difference between the three hearts in other Zelda games and the six hearts in Skyward Sword. In the games where you started with three hearts, enemies at the beginning only did a half a heart of damage. In Skyward Sword, the starting enemies do a whole heart of damage. The only difference is visual, making it only look like you have more health.
I like three hearts too... but I shudder to think of how horribly I would have done if I'd actually played Skyward Sword with three hearts. I would have died. A lot. XD