Activity log was really cool, I hate to see it ever not present. Wii U's was already a fair step down from what 3DS had though, so even if they had added it, probably wouldn't have been all that good. And 3DS was hurt by selling me so much hardware; so I could never get a full picture of my activity across all my 3DSes.
VC isn't a big deal to me. Unless they're gonna say, "hey, here are your Wii U and 3DS and maybe even Wii purchases, transfer them for free", than I have a hard time seeing myself care (they're not going to allow anything like that).
The syncing issue has potential to be a real big deal though. Does it happen when connected to the grip? If so that makes it a more big deal for me personally. Would expedite my purchase of a pro controller. If it's just when they're floating off on their own, unconnected, I can't see myself personally encountering it much.