I wouldn't have said the OoT bosses are more challenging than the TP ones (in general). Perhaps people are getting that impression because OoT was the first game many people played like that, and the people playing TP are generally made up of people who played OoT in the past (or games that have taken a similar formula) and are thus wise enough to know what to expect.
WindWaker bosses are definately less challenging though... In part I would guess it's because it's much easier to control the camera, which can occasionally be an issue when the L/Z-target system is also the only thing that allows the player to control the camera. In fact after the initial playthrough I don't think I really enjoy any of the WW bossfights apart from Jalhalla and the final Ganondorf battle.
I think I might get Monster Hunter Tri, I am not a big fan of the ridiculous amount of levelling up and "grinding" that games like it involve, in part because I tend to get sucked in for too long till I realise I am spending hours repeating the same thing over and over for little reward, but I mostly hear good about MHTri.
I would also like to put forward that Okami has a couple of pretty epic boss battles that have a similar "Zelda 3d boss" formula but still manage to be challenging (namely the 9 tailed fox and the final battle against the sphere thing) although I have only gone through them twice, perhaps if I repeated them as much as I have in Zelda games they would get mundane too.
