For me, the IR pointer in the Wiimote is the best thing about it, it's nearly perfect and nothing else has come close to being as good.
Ah, that. I would have agreed before Skyward Sword as I thoroughly enjoy aiming in Twilight Princess. Gyroscope aiming was more reliable to me as it didn't rely on line of sight. Holding the Wii remote slightly ajar tended to screw up the IR signal. If I wasn't so lazy, I'd boot up both Wii Zelda games to see if my memory is as good as I think it is.
And going off-topic is what we do at NWR.
Yeah, I know some people complained about it being "jittery" and things like that, but I didn't really experience those issues meself. I guess I just have a good setup for it, I could see it having potential problems for some people. In comparison, gyro pointing feels too sluggish to me, and it also feels very unintuitive with the GamePad since it's a huge controller and not made for pointing like the Wiimote is. It also needs to be recalibrated fairly often.
Oh, also, your example of an IR pointer game is a launch title. The pointer got better as the Wii went on, especially in games like The Conduit and Call of Duty which have a wealth of fine-tuning options to make it nearly perfect.
There may still be ways they could improve the pointing, though, such as using both IR and gyro or something. Could be complex to implement though.