I'm a Skyward Sword booster, and don't find the generally agreed upon annoying parts to be annoying (aside from the Tadtones sequence, but that's really just a blip in the scope of the whole game). Depending on how far you get, be aware that there are multiple ways to approach the repeating boss that make the fights more interesting, and these ways are not necessarily apparent. Also, there's a whole side-quest system involving various townsfolk that is basically hidden, but I found it very entertaining and that it gave bonus social texture to Skyloft.
On a technical note, I found the motion controls to work flawlessly on first playthrough, but years later on a second run with my brother we had fairly regular issues with the syncing/drifting. I looked it up and though it's anecdotal, it seems like your best bet is to use the integrated Motion Plus wiimote with fresh batteries (on second run I had a motion plus dongle and crummy over-the-hill rechargable batteries).