I really thought I would only play with the pro controller, but on my first sitting with the game I thought "Well, let's give the Gamepad a try once, then I'll switch next time..." Well, I'm just short of beating the game now some 35 hours later and I've only used the Gamepad. I really liked the map screen being available at all times when sailing, which is why I kept it for the early parts of the game. Once I got into heavy item switching, I really loved it. That on-the-fly ability to manage inventory and not have to pause is quite nice.
My only problem is forgetting I can still pause to manage inventory when I have to. I've been flustered in a room full of enemies and tried switching weapons to get hit a number of times. I still forget that I can pause and do this on the pad as has always been done in Zelda.
I also didn't think I would use the Miiverse features at all, but I got addicted to posting screencaps (mainly so I could save them later to my computer). It also solidified it when the Nintendo Gallery could be shared through the Tingle Bottles. That's a sidequest I never completed on the Gamecube, and it was nice to be able to this time through Miiverse help. I don't even know if that's really available through the Pro Controller, but I can't imagine it's as easy to do if it is.