I occasionally have similar problems and I am not sure why.
Usually what I do with the most success is hold the sync button on the wii for about 20 seconds. This is supposed to clear all the pairings the wii has stored. It may or may not help to remove the batteries in the wiimote for a period of time as well.
usually at least one of 5 wiimotes will sync after doing this.
Another thing to try, assuming you are softmodded, is to reinstall your softmod just in case something you installed is corrupted somehow. I have had some weird issues get resolved doing this even when a syscheck is not showing any issues. I simply take the modpack from the softmod guide, all 30 wads or so, and reinstall them with wiimod or something. This is the only part of the guide you really need to redo, but it may resolve some issues.
I have not modded my wii u due to various reasons and this is the one annoyance I have continuing to use both systems at the same time.