My problem with the bosses is not so much that their weaknesses are obvious, though that is a major complaint. My biggest issue is just how gosh darn easy it is to execute the needed attacks. I'm not saying the bosses should be so well protected that they're impossible to hit, but a bit of self-defense and some intellect goes a long way.
Also, I'd love to see more traditional swordfighting. Minibosses like the Darknut (epic) are so amazing because they don't employ silly gimmicks. It's Link and his sword and shield against a competent enemy with just a sword and shield. Other examples include things like the Lizalfos or Iron Knuckle in OoT, both of which I loved fighting. Darknuts and the final duel with Ganondorf in TP are my favorite combat experiences in Zelda games because it's straight out fighting, no gimmick weaknesses. Oh, forgot to mention, OoT's Dark Link, provided you use only the Master Sword, which I did. I loved that fight soooooo much. He was more challenging than Morpha. It's a problem when minibosses are harder than the temple's boss.
Oh yes, we also seriously need more overworld bosses and minibosses. King Bulblin was fun and all, but we need more of them, make Link feel like he's making a difference outside of obscure dungeons no ordinary citizen would enter anyways.